From 7e80c8e5edba7ad56adecd391c34e4bd5c158e84 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Fri, 19 Mar 2021 14:38:28 -0400 Subject: [PATCH 01/68] Update AnnotatedRecord.java --- .../org/cbioportal/models/AnnotatedRecord.java | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java b/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java index b0900fbf..00e29567 100644 --- a/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java +++ b/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java @@ -105,6 +105,12 @@ public AnnotatedRecord(String hugoSymbol, String tAltCount, String nRefCount, String nAltCount, + String GN_Immutable_Chromosome, + String GN_Immutable_Start_Position, + String GN_Immutable_End_Position, + String GN_Immutable_Reference_Allele, + String GN_Immutable_Tumor_Seq_Allele1, + String GN_Immutable_Tumor_Seq_Allele2, String hgvsc, String hgvsp, String hgvspShort, @@ -157,6 +163,12 @@ public AnnotatedRecord(String hugoSymbol, tAltCount, nRefCount, nAltCount, + GN_Immutable_Chromosome, + GN_Immutable_Start_Position, + GN_Immutable_End_Position, + GN_Immutable_Reference_Allele, + GN_Immutable_Tumor_Seq_Allele1, + GN_Immutable_Tumor_Seq_Allele2, additionalProperties); this.hgvsc = hgvsc; this.hgvsp = hgvsp; @@ -213,6 +225,12 @@ public AnnotatedRecord(MutationRecord mRecord) { this.tAltCount = mRecord.getT_ALT_COUNT(); this.nRefCount = mRecord.getN_REF_COUNT(); this.nAltCount = mRecord.getN_ALT_COUNT(); + this.GN_Immutable_Chromosome = mRecord.getCHROMOSOME(); + this.GN_Immutable_Start_Position = mRecord.getSTART_POSITION(); + this.GN_Immutable_End_Position = mRecord.getEND_POSITION(); + this.GN_Immutable_Reference_Allele = mRecord.getREFERENCE_ALLELE(); + this.GN_Immutable_Tumor_Seq_Allele1 = mRecord.getTUMOR_SEQ_ALLELE1(); + this.GN_Immutable_Tumor_Seq_Allele2 = mRecord.getTUMOR_SEQ_ALLELE2(); this.hgvsc = additionalProperties.get("HGVSc") != null ? additionalProperties.get("HGVSc") : ""; this.hgvsp = additionalProperties.get("HGVSp") != null ? additionalProperties.get("HGVSp") : ""; this.hgvspShort = additionalProperties.get("HGVSp_Short"); From cc72b6e3b379d1985462f6f9aa86facd6d547aa5 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Fri, 19 Mar 2021 14:40:50 -0400 Subject: [PATCH 02/68] Update GenomeNexusImpl.java --- .../org/cbioportal/annotator/internal/GenomeNexusImpl.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java index 05d904f1..cea9aa64 100644 --- a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java +++ b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java @@ -270,6 +270,12 @@ public AnnotatedRecord convertResponseToAnnotatedRecord(VariantAnnotation gnResp mRecord.getT_ALT_COUNT(), mRecord.getN_REF_COUNT(), mRecord.getN_ALT_COUNT(), + mRecord.getCHROMOSOME(), + mRecord.getSTART_POSITION(), + mRecord.getEND_POSITION(), + mRecord.getREFERENCE_ALLELE(), + mRecord.getTUMOR_SEQ_ALLELE1(), + mRecord.getTUMOR_SEQ_ALLELE2(), annotationUtil.resolveHgvsc(canonicalTranscript), annotationUtil.resolveHgvsp(canonicalTranscript), annotationUtil.resolveHgvspShort(canonicalTranscript), From c91cf4ca053df4527ca3c3b4e3e15ed50927f56b Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 12:17:03 -0400 Subject: [PATCH 03/68] Update GenomeNexusImpl.java --- .../annotator/internal/GenomeNexusImpl.java | 42 ++++++++++++++++--- 1 file changed, 36 insertions(+), 6 deletions(-) diff --git a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java index cea9aa64..961e6e3d 100644 --- a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java +++ b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java @@ -231,6 +231,36 @@ public AnnotatedRecord convertResponseToAnnotatedRecord(VariantAnnotation gnResp // variant attributes (pos,ref,alt1,alt2) to be mutable? } + String GN_Immutable_Chromosome_Value; + String GN_Immutable_Start_Position_Value; + String GN_Immutable_End_Position_Value; + String GN_Immutable_Reference_Allele_Value; + String GN_Immutable_Tumor_Seq_Allele1_Value; + String GN_Immutable_Tumor_Seq_Allele2_Value; + + GN_Immutable_Chromosome_Value = ((GN_Immutable_Chromosome_Value = mRecord.getGN_IMMUTABLE_CHROMOSOME()) != "") ? GN_Immutable_Chromosome_Value : mRecord.getCHROMOSOME(); + GN_Immutable_Start_Position_Value = ((GN_Immutable_Start_Position_Value = mRecord.getGN_IMMUTABLE_START_POSITION()) != "") ? GN_Immutable_Start_Position_Value : mRecord.getSTART_POSITION(); + GN_Immutable_End_Position_Value = ((GN_Immutable_End_Position_Value = mRecord.getGN_IMMUTABLE_END_POSITION()) != "") ? GN_Immutable_End_Position_Value : mRecord.getEND_POSITION(); + GN_Immutable_Reference_Allele_Value = ((GN_Immutable_Reference_Allele_Value = mRecord.getGN_IMMUTABLE_REFERENCE_ALLELE()) != "") ? GN_Immutable_Reference_Allele_Value : mRecord.getREFERENCE_ALLELE(); + GN_Immutable_Tumor_Seq_Allele1_Value = ((GN_Immutable_Tumor_Seq_Allele1_Value = mRecord.getGN_IMMUTABLE_TUMOR_SEQ_ALLELE1()) != "") ? GN_Immutable_Tumor_Seq_Allele1_Value : mRecord.getTUMOR_SEQ_ALLELE1(); + GN_Immutable_Tumor_Seq_Allele2_Value = ((GN_Immutable_Tumor_Seq_Allele2_Value = mRecord.getGN_IMMUTABLE_TUMOR_SEQ_ALLELE2()) != "") ? GN_Immutable_Tumor_Seq_Allele2_Value : mRecord.getTUMOR_SEQ_ALLELE2(); + + /* + String GN_Immutable_Chromosome_Value = mRecord.getCHROMOSOME(); + String GN_Immutable_Start_Position_Value = mRecord.getSTART_POSITION(); + String GN_Immutable_End_Position_Value = mRecord.getEND_POSITION(); + String GN_Immutable_Reference_Allele_Value = mRecord.getREFERENCE_ALLELE(); + String GN_Immutable_Tumor_Seq_Allele1_Value = mRecord.getTUMOR_SEQ_ALLELE1(); + String GN_Immutable_Tumor_Seq_Allele2_Value = mRecord.getTUMOR_SEQ_ALLELE2(); + + mRecord.getCHROMOSOME(), + mRecord.getSTART_POSITION(), + mRecord.getEND_POSITION(), + mRecord.getREFERENCE_ALLELE(), + mRecord.getTUMOR_SEQ_ALLELE1(), + mRecord.getTUMOR_SEQ_ALLELE2(), + */ + // annotate the record AnnotatedRecord annotatedRecord= new AnnotatedRecord(annotationUtil.resolveHugoSymbol(canonicalTranscript, mRecord, replace), annotationUtil.resolveEntrezGeneId(canonicalTranscript, mRecord, replace), @@ -270,12 +300,12 @@ public AnnotatedRecord convertResponseToAnnotatedRecord(VariantAnnotation gnResp mRecord.getT_ALT_COUNT(), mRecord.getN_REF_COUNT(), mRecord.getN_ALT_COUNT(), - mRecord.getCHROMOSOME(), - mRecord.getSTART_POSITION(), - mRecord.getEND_POSITION(), - mRecord.getREFERENCE_ALLELE(), - mRecord.getTUMOR_SEQ_ALLELE1(), - mRecord.getTUMOR_SEQ_ALLELE2(), + GN_Immutable_Chromosome_Value, + GN_Immutable_Start_Position_Value, + GN_Immutable_End_Position_Value, + GN_Immutable_Reference_Allele_Value, + GN_Immutable_Tumor_Seq_Allele1_Value, + GN_Immutable_Tumor_Seq_Allele2_Value, annotationUtil.resolveHgvsc(canonicalTranscript), annotationUtil.resolveHgvsp(canonicalTranscript), annotationUtil.resolveHgvspShort(canonicalTranscript), From c9f3f2ee6a5f1328ee8015264acaa06b14ff2a1b Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 12:17:34 -0400 Subject: [PATCH 04/68] Update GenomeNexusImpl.java --- .../annotator/internal/GenomeNexusImpl.java | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java index 961e6e3d..94d4109d 100644 --- a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java +++ b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java @@ -245,22 +245,6 @@ public AnnotatedRecord convertResponseToAnnotatedRecord(VariantAnnotation gnResp GN_Immutable_Tumor_Seq_Allele1_Value = ((GN_Immutable_Tumor_Seq_Allele1_Value = mRecord.getGN_IMMUTABLE_TUMOR_SEQ_ALLELE1()) != "") ? GN_Immutable_Tumor_Seq_Allele1_Value : mRecord.getTUMOR_SEQ_ALLELE1(); GN_Immutable_Tumor_Seq_Allele2_Value = ((GN_Immutable_Tumor_Seq_Allele2_Value = mRecord.getGN_IMMUTABLE_TUMOR_SEQ_ALLELE2()) != "") ? GN_Immutable_Tumor_Seq_Allele2_Value : mRecord.getTUMOR_SEQ_ALLELE2(); - /* - String GN_Immutable_Chromosome_Value = mRecord.getCHROMOSOME(); - String GN_Immutable_Start_Position_Value = mRecord.getSTART_POSITION(); - String GN_Immutable_End_Position_Value = mRecord.getEND_POSITION(); - String GN_Immutable_Reference_Allele_Value = mRecord.getREFERENCE_ALLELE(); - String GN_Immutable_Tumor_Seq_Allele1_Value = mRecord.getTUMOR_SEQ_ALLELE1(); - String GN_Immutable_Tumor_Seq_Allele2_Value = mRecord.getTUMOR_SEQ_ALLELE2(); - - mRecord.getCHROMOSOME(), - mRecord.getSTART_POSITION(), - mRecord.getEND_POSITION(), - mRecord.getREFERENCE_ALLELE(), - mRecord.getTUMOR_SEQ_ALLELE1(), - mRecord.getTUMOR_SEQ_ALLELE2(), - */ - // annotate the record AnnotatedRecord annotatedRecord= new AnnotatedRecord(annotationUtil.resolveHugoSymbol(canonicalTranscript, mRecord, replace), annotationUtil.resolveEntrezGeneId(canonicalTranscript, mRecord, replace), From 812e9be010b58acc17ed10ce06fcd3d6a4614428 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 12:18:12 -0400 Subject: [PATCH 05/68] Update AnnotatedRecord.java --- .../java/org/cbioportal/models/AnnotatedRecord.java | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java b/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java index 00e29567..3605cea1 100644 --- a/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java +++ b/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java @@ -225,12 +225,12 @@ public AnnotatedRecord(MutationRecord mRecord) { this.tAltCount = mRecord.getT_ALT_COUNT(); this.nRefCount = mRecord.getN_REF_COUNT(); this.nAltCount = mRecord.getN_ALT_COUNT(); - this.GN_Immutable_Chromosome = mRecord.getCHROMOSOME(); - this.GN_Immutable_Start_Position = mRecord.getSTART_POSITION(); - this.GN_Immutable_End_Position = mRecord.getEND_POSITION(); - this.GN_Immutable_Reference_Allele = mRecord.getREFERENCE_ALLELE(); - this.GN_Immutable_Tumor_Seq_Allele1 = mRecord.getTUMOR_SEQ_ALLELE1(); - this.GN_Immutable_Tumor_Seq_Allele2 = mRecord.getTUMOR_SEQ_ALLELE2(); + this.GN_Immutable_Chromosome = mRecord.getGN_IMMUTABLE_CHROMOSOME(); + this.GN_Immutable_Start_Position = mRecord.getGN_IMMUTABLE_START_POSITION(); + this.GN_Immutable_End_Position = mRecord.getGN_IMMUTABLE_END_POSITION(); + this.GN_Immutable_Reference_Allele = mRecord.getGN_IMMUTABLE_REFERENCE_ALLELE(); + this.GN_Immutable_Tumor_Seq_Allele1 = mRecord.getGN_IMMUTABLE_TUMOR_SEQ_ALLELE1(); + this.GN_Immutable_Tumor_Seq_Allele2 = mRecord.getGN_IMMUTABLE_TUMOR_SEQ_ALLELE2(); this.hgvsc = additionalProperties.get("HGVSc") != null ? additionalProperties.get("HGVSc") : ""; this.hgvsp = additionalProperties.get("HGVSp") != null ? additionalProperties.get("HGVSp") : ""; this.hgvspShort = additionalProperties.get("HGVSp_Short"); From ddbd7f2c49d5a72c70ddf8f46d6154107b509ed3 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 12:18:51 -0400 Subject: [PATCH 06/68] Update MutationRecord.java --- .../org/cbioportal/models/MutationRecord.java | 70 ++++++++++++++++++- 1 file changed, 69 insertions(+), 1 deletion(-) diff --git a/annotator/src/main/java/org/cbioportal/models/MutationRecord.java b/annotator/src/main/java/org/cbioportal/models/MutationRecord.java index 5c6770b3..89751fcb 100644 --- a/annotator/src/main/java/org/cbioportal/models/MutationRecord.java +++ b/annotator/src/main/java/org/cbioportal/models/MutationRecord.java @@ -77,6 +77,12 @@ public class MutationRecord { protected String tAltCount; protected String nRefCount; protected String nAltCount; + protected String GN_Immutable_Chromosome; + protected String GN_Immutable_Start_Position; + protected String GN_Immutable_End_Position; + protected String GN_Immutable_Reference_Allele; + protected String GN_Immutable_Tumor_Seq_Allele1; + protected String GN_Immutable_Tumor_Seq_Allele2; protected Map additionalProperties = new LinkedHashMap<>(); protected List header = new ArrayList<>(); @@ -93,7 +99,9 @@ public MutationRecord(String hugoSymbol, String entrezGeneId, String center, Str String verificationStatus, String validationStatus, String mutationStatus, String sequencingPhase, String sequencingSource, String validationMethod, String score, String bamFile, String sequencer, String tumorSampleUUID, String matchedNormSampleUUID, String tRefCount, String tAltCount, - String nRefCount, String nAltCount, Map additionalProperties) { + String nRefCount, String nAltCount, String GN_Immutable_Chromosome, String GN_Immutable_Start_Position, + String GN_Immutable_End_Position, String GN_Immutable_Reference_Allele, String GN_Immutable_Tumor_Seq_Allele1, + String GN_Immutable_Tumor_Seq_Allele2, Map additionalProperties) { this.hugoSymbol = hugoSymbol; this.entrezGeneId = entrezGeneId; @@ -133,6 +141,12 @@ public MutationRecord(String hugoSymbol, String entrezGeneId, String center, Str this.tAltCount = tAltCount; this.nRefCount = nRefCount; this.nAltCount = nAltCount; + this.GN_Immutable_Chromosome = GN_Immutable_Chromosome; + this.GN_Immutable_Start_Position = GN_Immutable_Start_Position; + this.GN_Immutable_End_Position = GN_Immutable_End_Position; + this.GN_Immutable_Reference_Allele = GN_Immutable_Reference_Allele; + this.GN_Immutable_Tumor_Seq_Allele1 = GN_Immutable_Tumor_Seq_Allele1; + this.GN_Immutable_Tumor_Seq_Allele2 = GN_Immutable_Tumor_Seq_Allele2; this.additionalProperties = additionalProperties; initHeader(); } @@ -441,6 +455,54 @@ public void setN_ALT_COUNT(String nAltCount) { this.nAltCount = nAltCount; } + public String getGN_IMMUTABLE_CHROMOSOME() { + return this.GN_Immutable_Chromosome == null ? "" : this.GN_Immutable_Chromosome; + } + + public void setGN_IMMUTABLE_CHROMOSOME(String GN_Immutable_Chromosome) { + this.GN_Immutable_Chromosome = GN_Immutable_Chromosome; + } + + public String getGN_IMMUTABLE_START_POSITION() { + return this.GN_Immutable_Start_Position == null ? "" : this.GN_Immutable_Start_Position; + } + + public void setGN_IMMUTABLE_START_POSITION(String GN_Immutable_Start_Position) { + this.GN_Immutable_Start_Position = GN_Immutable_Start_Position; + } + + public String getGN_IMMUTABLE_END_POSITION() { + return this.GN_Immutable_End_Position == null ? "" : this.GN_Immutable_End_Position; + } + + public void setGN_IMMUTABLE_END_POSITION(String GN_Immutable_End_Position) { + this.GN_Immutable_End_Position = GN_Immutable_End_Position; + } + + public String getGN_IMMUTABLE_REFERENCE_ALLELE() { + return this.GN_Immutable_Reference_Allele == null ? "" : this.GN_Immutable_Reference_Allele; + } + + public void setGN_IMMUTABLE_REFERENCE_ALLELE(String GN_Immutable_Reference_Allele) { + this.GN_Immutable_Reference_Allele = GN_Immutable_Reference_Allele; + } + + public String getGN_IMMUTABLE_TUMOR_SEQ_ALLELE1() { + return this.GN_Immutable_Tumor_Seq_Allele1 == null ? "" : this.GN_Immutable_Tumor_Seq_Allele1; + } + + public void setGN_IMMUTABLE_TUMOR_SEQ_ALLELE1(String GN_Immutable_Tumor_Seq_Allele1) { + this.GN_Immutable_Tumor_Seq_Allele1 = GN_Immutable_Tumor_Seq_Allele1; + } + + public String getGN_IMMUTABLE_TUMOR_SEQ_ALLELE2() { + return this.GN_Immutable_Tumor_Seq_Allele2 == null ? "" : this.GN_Immutable_Tumor_Seq_Allele2; + } + + public void setGN_IMMUTABLE_TUMOR_SEQ_ALLELE2(String GN_Immutable_Tumor_Seq_Allele2) { + this.GN_Immutable_Tumor_Seq_Allele2 = GN_Immutable_Tumor_Seq_Allele2; + } + public void addAdditionalProperty(String property, String value) { this.additionalProperties.put(property, value); } @@ -523,5 +585,11 @@ public void initHeader() { header.add("t_alt_count"); header.add("n_ref_count"); header.add("n_alt_count"); + header.add("GN_Immutable_Chromosome"); + header.add("GN_Immutable_Start_Position"); + header.add("GN_Immutable_End_Position"); + header.add("GN_Immutable_Reference_Allele"); + header.add("GN_Immutable_Tumor_Seq_Allele1"); + header.add("GN_Immutable_Tumor_Seq_Allele2"); } } From 1e005851b7bd1c46d7ee7b661aa78c209bb6df28 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 14:16:58 -0400 Subject: [PATCH 07/68] Added GN_Immutable --- .../src/main/java/org/cbioportal/models/AnnotatedRecord.java | 1 + 1 file changed, 1 insertion(+) diff --git a/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java b/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java index 3605cea1..5c7e053f 100644 --- a/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java +++ b/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java @@ -474,3 +474,4 @@ private void addAnnotatedFieldsToHeader() { header.add(header.indexOf("Variant_Classification"), "Consequence"); } } + From cb52a6ee91ca032aa6c1b870e52b68c34a69701f Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 14:17:11 -0400 Subject: [PATCH 08/68] Added GN_Immutable --- .../src/main/java/org/cbioportal/models/MutationRecord.java | 1 + 1 file changed, 1 insertion(+) diff --git a/annotator/src/main/java/org/cbioportal/models/MutationRecord.java b/annotator/src/main/java/org/cbioportal/models/MutationRecord.java index 89751fcb..835e6297 100644 --- a/annotator/src/main/java/org/cbioportal/models/MutationRecord.java +++ b/annotator/src/main/java/org/cbioportal/models/MutationRecord.java @@ -593,3 +593,4 @@ public void initHeader() { header.add("GN_Immutable_Tumor_Seq_Allele2"); } } + From 5047f5ea630cc82116ce62fabc3efca5d0abfe58 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 14:17:29 -0400 Subject: [PATCH 09/68] Added GN_Immutable --- .../java/org/cbioportal/annotator/internal/GenomeNexusImpl.java | 1 + 1 file changed, 1 insertion(+) diff --git a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java index 94d4109d..0ec9deca 100644 --- a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java +++ b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java @@ -557,3 +557,4 @@ public int compare(GenomicLocation gl1, GenomicLocation gl2) { } }; } + From 473457094243ba9419563652a74104cb091fc20f Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 14:17:42 -0400 Subject: [PATCH 10/68] Added GN_Immutable --- .../java/org/cbioportal/annotator/internal/GenomeNexusImpl.java | 1 - 1 file changed, 1 deletion(-) diff --git a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java index 0ec9deca..94d4109d 100644 --- a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java +++ b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java @@ -557,4 +557,3 @@ public int compare(GenomicLocation gl1, GenomicLocation gl2) { } }; } - From ea8a7089db03bd2e1f036bcb0e48209c071933f4 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 14:18:04 -0400 Subject: [PATCH 11/68] Added GN_Immutable --- .../src/main/java/org/cbioportal/models/AnnotatedRecord.java | 1 - 1 file changed, 1 deletion(-) diff --git a/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java b/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java index 5c7e053f..3605cea1 100644 --- a/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java +++ b/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java @@ -474,4 +474,3 @@ private void addAnnotatedFieldsToHeader() { header.add(header.indexOf("Variant_Classification"), "Consequence"); } } - From fcf34f63468741823ebcb7357ded20c9ccc2b711 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 14:18:16 -0400 Subject: [PATCH 12/68] Added GN_Immutable --- .../src/main/java/org/cbioportal/models/MutationRecord.java | 1 - 1 file changed, 1 deletion(-) diff --git a/annotator/src/main/java/org/cbioportal/models/MutationRecord.java b/annotator/src/main/java/org/cbioportal/models/MutationRecord.java index 835e6297..89751fcb 100644 --- a/annotator/src/main/java/org/cbioportal/models/MutationRecord.java +++ b/annotator/src/main/java/org/cbioportal/models/MutationRecord.java @@ -593,4 +593,3 @@ public void initHeader() { header.add("GN_Immutable_Tumor_Seq_Allele2"); } } - From cab8e798e40b29c283f65b689fca2910a649cae1 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 15:30:49 -0400 Subject: [PATCH 13/68] GN_Immutable --- test/data/corner_cases.out.mskcc.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/data/corner_cases.out.mskcc.txt b/test/data/corner_cases.out.mskcc.txt index 5964fd3c..6b988dbd 100644 --- a/test/data/corner_cases.out.mskcc.txt +++ b/test/data/corner_cases.out.mskcc.txt @@ -1,5 +1,5 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - 7 116411872 116411900 TAACAAGCTCTTTCTTTCTCTCTGTTTTA - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 8 17796382 17796383 AC GT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS From 497d288b2841ab5277b9aad7b7a55b99d1ca10f0 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 15:31:05 -0400 Subject: [PATCH 14/68] Update corner_cases.out.uniprot.txt --- test/data/corner_cases.out.uniprot.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/data/corner_cases.out.uniprot.txt b/test/data/corner_cases.out.uniprot.txt index c34599e5..472c96c9 100644 --- a/test/data/corner_cases.out.uniprot.txt +++ b/test/data/corner_cases.out.uniprot.txt @@ -1,5 +1,5 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - 7 116411872 116411900 TAACAAGCTCTTTCTTTCTCTCTGTTTTA - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 8 17796382 17796383 AC GT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS From f8f66763a0f8ec7addae3c3d29552cd8ad7a6282 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 15:31:19 -0400 Subject: [PATCH 15/68] GN_Immutable --- test/data/corner_cases.out.uniprot.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/test/data/corner_cases.out.uniprot.txt b/test/data/corner_cases.out.uniprot.txt index 472c96c9..725343c0 100644 --- a/test/data/corner_cases.out.uniprot.txt +++ b/test/data/corner_cases.out.uniprot.txt @@ -3,3 +3,4 @@ Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - 7 116411872 116411900 TAACAAGCTCTTTCTTTCTCTCTGTTTTA - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 8 17796382 17796383 AC GT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS + From a483f20c329895a3569027eaa9fcadbf144c0756 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 15:31:26 -0400 Subject: [PATCH 16/68] GN_Immutable --- test/data/corner_cases.out.uniprot.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/test/data/corner_cases.out.uniprot.txt b/test/data/corner_cases.out.uniprot.txt index 725343c0..472c96c9 100644 --- a/test/data/corner_cases.out.uniprot.txt +++ b/test/data/corner_cases.out.uniprot.txt @@ -3,4 +3,3 @@ Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - 7 116411872 116411900 TAACAAGCTCTTTCTTTCTCTCTGTTTTA - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 8 17796382 17796383 AC GT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS - From 5146cf2ac2813cdd424970f378739621efb2d7db Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 15:31:45 -0400 Subject: [PATCH 17/68] GN_Immutable --- test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt b/test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt index bc4cbdd1..00fa8c00 100644 --- a/test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt +++ b/test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS -KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A 8 17796382 17796383 AC AAC GT ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS +KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 12 49435045 49435045 G C - ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 8 17796381 17796383 AAC AAC AGT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS From 8f713d30285493298d98f19c2b239fb44f386e2e Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 15:32:03 -0400 Subject: [PATCH 18/68] GN_Immutable --- .../corner_cases.two_tumor_seq_allele.out.uniprot.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt b/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt index 1f018a0f..663f7478 100644 --- a/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt +++ b/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS -KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A 8 17796382 17796383 AC AAC GT ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS +KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 12 49435045 49435045 G C - ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 8 17796381 17796383 AAC AAC AGT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS From 085a304a492e3d53c99d9a97ec5fc2df5d952c80 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 15:32:20 -0400 Subject: [PATCH 19/68] GN_Immutable --- .../data_mutations_extended_100.out.mskcc.txt | 200 +++++++++--------- 1 file changed, 100 insertions(+), 100 deletions(-) diff --git a/test/data/data_mutations_extended_100.out.mskcc.txt b/test/data/data_mutations_extended_100.out.mskcc.txt index c90ad22d..74bb5c33 100644 --- a/test/data/data_mutations_extended_100.out.mskcc.txt +++ b/test/data/data_mutations_extended_100.out.mskcc.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000298171.2:c.154C>A p.Pro52Thr p.P52T ENST00000298171 NM_000369.2 52 Ccc/Acc 1/10 SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000274335.5:c.1746-8_1748del p.X582_splice ENST00000274335 582 13/15 SUCCESS -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000397332.2:c.851T>G p.Ile284Ser p.I284S ENST00000397332 NM_001033082.2 284 aTt/aGt 3/3 SUCCESS -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000274335.5:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000274335 446 -/A 10/15 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000320356.2:c.848C>T p.Thr283Met p.T283M ENST00000320356 NM_004456.4 283 aCg/aTg 8/20 SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS +ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS +PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS +MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS +FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS +FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS +NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS +NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS +KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000298171.2:c.154C>A p.Pro52Thr p.P52T ENST00000298171 NM_000369.2 52 Ccc/Acc 1/10 SUCCESS +AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS +TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS +RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS +NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS +TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS +ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS +CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS +GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS +LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS +U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS +BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS +PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS +BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS +ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000274335.5:c.1746-8_1748del p.X582_splice ENST00000274335 582 13/15 SUCCESS +PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS +LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS +IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS +ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS +MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000397332.2:c.851T>G p.Ile284Ser p.I284S ENST00000397332 NM_001033082.2 284 aTt/aGt 3/3 SUCCESS +POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS +TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS +NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS +ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS +RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS +FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS +FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS +BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS +BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS +BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS +BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS +BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS +BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS +CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS +KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS +AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS +BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS +NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS +ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS +PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS +NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS +PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000274335.5:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000274335 446 -/A 10/15 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS +FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS +NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS +CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS +FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 A A CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS +MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS +NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS +TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS +TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS +PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS +BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS +SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS +PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS +FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS +SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000320356.2:c.848C>T p.Thr283Met p.T283M ENST00000320356 NM_004456.4 283 aCg/aTg 8/20 SUCCESS +MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS +IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS +KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS +KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS +FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS +FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS +FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS From f2f2350c0b39f94f04b205244c11130c277f3f50 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 15:32:37 -0400 Subject: [PATCH 20/68] GN_Immutable --- ...ded_100.out.uniprot.nucleotide_context.txt | 200 +++++++++--------- 1 file changed, 100 insertions(+), 100 deletions(-) diff --git a/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt b/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt index 6df872be..a69cb18e 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Ref_Tri Var_Tri Annotation_Status -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 CAT CTT SUCCESS -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 CAC CGC SUCCESS -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 GGC GAC SUCCESS -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 TCT TGT SUCCESS -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 CCG CAG SUCCESS -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 GTG GCG SUCCESS -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 CCG CTG SUCCESS -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 CGA CAA SUCCESS -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 GCA GTA SUCCESS -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 CGG CAG SUCCESS -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 GCC GAC SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 TCC TTC SUCCESS -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 CGG CAG SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 CGG CAG SUCCESS -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 TCG TTG SUCCESS -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 GCC GTC SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 CTC CAC SUCCESS -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 TCC TGC SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 CCA CGA SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 GTC GAC SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 CGA CAA SUCCESS -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 GTT GCT SUCCESS -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 TCT TAT SUCCESS -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 ACG AGG SUCCESS -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 ATT ACT SUCCESS -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 GCA GAA SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 GGG GCG SUCCESS -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 CGC CAC SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 AGG AAG SUCCESS -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 TAT TGT SUCCESS -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 TGC TAC SUCCESS -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 AAT ACT SUCCESS -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 GGT GCT SUCCESS -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 GCC GAC SUCCESS -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 AGA ATA SUCCESS -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 TCA TGA SUCCESS -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.938G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 TCA TGA SUCCESS -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 CGA CAA SUCCESS -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 AGA ACA SUCCESS -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 TCA TTA SUCCESS -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 TCA TTA SUCCESS -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 TCA TAA SUCCESS -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 TCT TGT SUCCESS -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 TCA TGA SUCCESS -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 TCA TGA SUCCESS -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 CGT CAT SUCCESS -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 CTT CCT SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 ATA ACA SUCCESS -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 ACG ATG SUCCESS -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 TCA TTA SUCCESS -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 AGA AAA SUCCESS -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 AGA AAA SUCCESS -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 TCC TTC SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 AGG AAG SUCCESS -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 CGC CAC SUCCESS -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 GGC GTC SUCCESS -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 GTA GCA SUCCESS -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 GGA GTA SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 TGT TCT SUCCESS -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 TCT TTT SUCCESS -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 TCG TGG SUCCESS -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 CGG CAG SUCCESS -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 GAT GGT SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 CAT CGT SUCCESS -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 GTT GCT SUCCESS -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 AGG AAG SUCCESS -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 TGG TCG SUCCESS -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 TCA TGA SUCCESS -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 GCG GGG SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 CGT CAT SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 GAG GTG SUCCESS -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 ATT AGT SUCCESS -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 AGA ACA SUCCESS -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 GGA GCA SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 AGG AAG SUCCESS -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 CCA CTA SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 TCC TTC SUCCESS -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 TCA TGA SUCCESS -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 TCT TGT SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS +ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS +PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS +MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS +FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS +FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS +NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS +NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS +KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS +AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS +TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS +RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS +NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS +TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS +ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS +CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS +GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS +LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS +U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS +BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS +PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS +BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS +ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS +PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS +LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS +IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS +ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS +MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS +POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS +TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS +NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS +ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS +RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS +FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS +FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS +BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS +BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS +BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS +BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS +BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS +BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS +CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS +KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS +AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS +BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS +NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS +ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS +PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS +NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS +PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS +FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS +NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS +CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS +FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 A A CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS +MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS +NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS +TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS +TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS +PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS +BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS +SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS +PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS +FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS +SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS +MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS +IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS +KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS +KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS +FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS +FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS +FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS From c99c899144629b868e84fb540d5f29600f058d8a Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 15:32:53 -0400 Subject: [PATCH 21/68] GN_Immutable --- ...ata_mutations_extended_100.out.uniprot.txt | 200 +++++++++--------- 1 file changed, 100 insertions(+), 100 deletions(-) diff --git a/test/data/data_mutations_extended_100.out.uniprot.txt b/test/data/data_mutations_extended_100.out.uniprot.txt index a8482108..a69cb18e 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS +ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS +PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS +MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS +FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS +FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS +NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS +NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS +KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS +AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS +TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS +RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS +NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS +TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS +ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS +CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS +GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS +LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS +U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS +BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS +PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS +BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS +ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS +PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS +LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS +IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS +ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS +MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS +POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS +TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS +NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS +ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS +RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS +FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS +FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS +BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS +BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS +BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS +BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS +BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS +BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS +CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS +KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS +AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS +BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS +NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS +ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS +PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS +NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS +PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS +FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS +NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS +CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS +FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 A A CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS +MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS +NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS +TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS +TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS +PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS +BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS +SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS +PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS +FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS +SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS +MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS +IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS +KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS +KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS +FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS +FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS +FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS From 7fdc70b8f9c6af32b4b73f7779388d91b8dba840 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 15:33:09 -0400 Subject: [PATCH 22/68] GN_Immutable --- test/data/minimal_example.out.uniprot.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/data/minimal_example.out.uniprot.txt b/test/data/minimal_example.out.uniprot.txt index 6d3ee305..e7f56cc9 100644 --- a/test/data/minimal_example.out.uniprot.txt +++ b/test/data/minimal_example.out.uniprot.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS -EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 SUCCESS -EGFR 1956 GRCh37 7 55242468 55242486 + protein_altering_variant In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G 3 178916927 178916939 TAGGCAACCGTGA G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS +EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T 7 55220240 55220240 G T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 SUCCESS +EGFR 1956 GRCh37 7 55242468 55242486 + protein_altering_variant In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA 7 55242467 55242486 AATTAAGAGAAGCAACATCT AGCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 SUCCESS From 83182dce4b94f930d92e1a851dfd08721cc9f135 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 15:33:26 -0400 Subject: [PATCH 23/68] GN_Immutable --- test/data/my_variant_info_corner_cases.out.uniprot.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/data/my_variant_info_corner_cases.out.uniprot.txt b/test/data/my_variant_info_corner_cases.out.uniprot.txt index 336c3387..74a3cf6a 100644 --- a/test/data/my_variant_info_corner_cases.out.uniprot.txt +++ b/test/data/my_variant_info_corner_cases.out.uniprot.txt @@ -1,4 +1,4 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF Annotation_Status -BARD1 580 GRCh37 2 215645503 215645523 + inframe_deletion In_Frame_Del DEL TGGTGAAGAACATTCAGGCAA - - rs28997575 ENST00000260947.4:c.1075_1095del p.Leu359_Pro365del p.L359_P365del ENST00000260947 NM_000465.2 359 TTGCCTGAATGTTCTTCACCA/- 4/11 0.0288928 0.0431947 0.0336575 0.012004 0.0438969 0.00355757 0.0178879 0.0324421 0.0705371 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +BARD1 580 GRCh37 2 215645503 215645523 + inframe_deletion In_Frame_Del DEL TGGTGAAGAACATTCAGGCAA - - rs28997575 2 215645503 215645523 TGGTGAAGAACATTCAGGCAA - ENST00000260947.4:c.1075_1095del p.Leu359_Pro365del p.L359_P365del ENST00000260947 NM_000465.2 359 TTGCCTGAATGTTCTTCACCA/- 4/11 SUCCESS From 3a5939ce5bb7490395a0b972cb5849270244fde5 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 16:47:35 -0400 Subject: [PATCH 24/68] Update corner_cases.out.mskcc.txt From a7286abb7237bed9b50504338459c3bfcc965a90 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 16:47:45 -0400 Subject: [PATCH 25/68] Update corner_cases.out.uniprot.txt From 39b277317fc1ae901d588e027b4a1833e5ed3aaf Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 16:47:54 -0400 Subject: [PATCH 26/68] Update corner_cases.two_tumor_seq_allele.out.mskcc.txt From bc1333aa34df14ae254b7b563e7c2feedcd2a53f Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 16:48:05 -0400 Subject: [PATCH 27/68] Update corner_cases.two_tumor_seq_allele.out.uniprot.txt From aac733ff337f08f0d6c5455793100b7e23eb1b2b Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 16:48:16 -0400 Subject: [PATCH 28/68] Update data_mutations_extended_100.out.mskcc.txt From da7638fc3dd0b807fb74a2a53fc9d9effa7510d6 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 16:48:27 -0400 Subject: [PATCH 29/68] Update data_mutations_extended_100.out.uniprot.nucleotide_context.txt From 023c9403f03220223650580131a225c9f01a5401 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 16:48:39 -0400 Subject: [PATCH 30/68] Update data_mutations_extended_100.out.uniprot.txt From 7103770fd01cff295d779bc3b2d1ce17ede43312 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 16:48:48 -0400 Subject: [PATCH 31/68] Update minimal_example.out.uniprot.txt From 69ec00abedfdb4c32e0c2531555dcc9157821373 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 16:48:59 -0400 Subject: [PATCH 32/68] Update my_variant_info_corner_cases.out.uniprot.txt From b2011a9bdab9ab1f2d86244d4aaf71c879ae1615 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sat, 20 Mar 2021 16:57:57 -0400 Subject: [PATCH 33/68] GN_Immutable --- test/data/data_mutations_extended_100.in.txt | 200 +++++++++---------- 1 file changed, 100 insertions(+), 100 deletions(-) diff --git a/test/data/data_mutations_extended_100.in.txt b/test/data/data_mutations_extended_100.in.txt index 941bce1e..9b436574 100644 --- a/test/data/data_mutations_extended_100.in.txt +++ b/test/data/data_mutations_extended_100.in.txt @@ -1,100 +1,100 @@ -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427delGCCAAGACCTGCCCTG p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dupG p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983delC p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dupT p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492delAGCT p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748delTTTTTCAGGTG p.X582_splice ENST00000521381 NM_181523.2 -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dupA p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.938G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108delG p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118delGACCTTCAGAGCAAATGTC p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dupA p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag -FGFR3 37 4 1806090 1806090 In_Frame_Ins DEL A A CACT P-0000056-T01-IM3 816 370 -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943delC p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delCGCTGGAGACCTTACGACinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons +SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt +ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg +PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc +MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt +FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg +FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg +NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg +NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg +MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA +MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg +TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc +AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag +TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg +RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg +NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa +TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427delGCCAAGACCTGCCCTG p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg +ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag +ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc +CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg +RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg +GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dupG p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G +LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc +LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga +U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc +BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983delC p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct +LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dupT p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T +CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt +PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga +BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt +ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492delAGCT p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at +PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748delTTTTTCAGGTG p.X582_splice ENST00000521381 NM_181523.2 +PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dupA p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg +PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag +LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct +IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 +CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat +ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc +MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt +POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG +TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT +NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att +ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa +RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.938G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat +FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga +FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat +BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag +BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa +BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa +BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc +BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG +BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac +CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg +KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108delG p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt +FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt +AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt +BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118delGACCTTCAGAGCAAATGTC p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag +TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt +NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA +ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt +PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa +NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag +PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dupA p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 +BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc +FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca +NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc +CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag +FGFR3 37 4 1806090 1806090 In_Frame_Ins DEL A A CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag +BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa +MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt +NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag +TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga +TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg +PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt +PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt +BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa +SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943delC p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc +MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delCGCTGGAGACCTTACGACinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg +PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt +FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac +SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg +EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg +MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg +IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG +KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG +KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 +EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag +FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc +FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac +FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat From 01ba663ae29a9dcada5c6361b1f6a874a19f585d Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sun, 21 Mar 2021 19:34:10 -0400 Subject: [PATCH 34/68] Entrez ID issue --- ...ata_mutations_extended_100.out.uniprot.txt | 202 +++++++++--------- 1 file changed, 101 insertions(+), 101 deletions(-) diff --git a/test/data/data_mutations_extended_100.out.uniprot.txt b/test/data/data_mutations_extended_100.out.uniprot.txt index a69cb18e..9b6985c8 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.txt @@ -1,102 +1,102 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT -#isoform: uniprot +#genome_nexus_version: 0-unknown-version-SNAPSHOT +#isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS -AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS -POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 A A CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS -MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS -IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS +ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 29-Jul SUCCESS +PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5-May SUCCESS +MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS +FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS +FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 30-Nov SUCCESS +NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS +NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 30-Apr SUCCESS +KMT2C GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +KMT2D GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 11-Feb SUCCESS +AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 15-Apr SUCCESS +TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg Nov-42 SUCCESS +RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 10-May SUCCESS +NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa Mar-33 SUCCESS +TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 11-May SUCCESS +ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 21-Oct SUCCESS +ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8-Aug SUCCESS +CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 8-May SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 11-Jul SUCCESS +RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 10-May SUCCESS +GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 6-May SUCCESS +LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 7-Apr SUCCESS +LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 7-Jan SUCCESS +U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 8-Jul SUCCESS +BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 17-Nov SUCCESS +LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 8-Jun SUCCESS +CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 15-Mar SUCCESS +PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 9-May SUCCESS +BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 15-Oct SUCCESS +ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS +PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 9-Aug SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 11-Jul SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 11-Jul SUCCESS +PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 21-Oct SUCCESS +LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 7-Mar SUCCESS +IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8-Aug SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS +ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 11-Jul SUCCESS +MYCL GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2-Feb SUCCESS +POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS +TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 11-Jul SUCCESS +NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS +ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 20-Jan SUCCESS +RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4-Apr SUCCESS +FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 27-Oct SUCCESS +FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 18-Jun SUCCESS +BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 22-Mar SUCCESS +BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 22-Mar SUCCESS +BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 22-Mar SUCCESS +BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 22-Mar SUCCESS +BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 22-Mar SUCCESS +BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 22-Mar SUCCESS +CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS +KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 21-Nov SUCCESS +AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 15-Oct SUCCESS +BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 17-Mar SUCCESS +TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 11-Aug SUCCESS +NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 7-Mar SUCCESS +ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS +PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 21-Feb SUCCESS +NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS +PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 16-Nov SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 17-Apr SUCCESS +FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 18-Mar SUCCESS +NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS +CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 3-Feb SUCCESS +FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 17-Aug SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 21-Oct SUCCESS +BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11-Nov SUCCESS +MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS +NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS +TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 11-Oct SUCCESS +TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 11-Jun SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 11-Jul SUCCESS +PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS +PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 9-Jul SUCCESS +BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS +SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12-Dec SUCCESS +MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 3-Jan SUCCESS +PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS +FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 27-Oct SUCCESS +SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 11-Jul SUCCESS +EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 20-Aug SUCCESS +MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 11-Aug SUCCESS +IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS +KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 6-Mar SUCCESS +KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 16-Mar SUCCESS +FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 17-Aug SUCCESS +FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS +FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS From d3767107f2414091bb456baa02b2ed1e93257169 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sun, 21 Mar 2021 20:16:10 -0400 Subject: [PATCH 35/68] Update data_mutations_extended_100.out.uniprot.txt --- ...ata_mutations_extended_100.out.uniprot.txt | 146 +++++++++--------- 1 file changed, 73 insertions(+), 73 deletions(-) diff --git a/test/data/data_mutations_extended_100.out.uniprot.txt b/test/data/data_mutations_extended_100.out.uniprot.txt index 9b6985c8..3129e08a 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.txt @@ -1,102 +1,102 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT -#isoform: uniprot +#genome_nexus_version: 0-unknown-version-SNAPSHOT +#isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 29-Jul SUCCESS -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5-May SUCCESS +ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS +PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 30-Nov SUCCESS +FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 30-Apr SUCCESS -KMT2C GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -KMT2D GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 11-Feb SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 15-Apr SUCCESS -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg Nov-42 SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 10-May SUCCESS -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa Mar-33 SUCCESS -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 11-May SUCCESS +NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS +MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS +AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS +TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS +RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS +NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS +TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 21-Oct SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8-Aug SUCCESS -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 8-May SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 11-Jul SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 10-May SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 6-May SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 7-Apr SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 7-Jan SUCCESS -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 8-Jul SUCCESS -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 17-Nov SUCCESS -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 8-Jun SUCCESS -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 15-Mar SUCCESS -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 9-May SUCCESS -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 15-Oct SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS +CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS +GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS +LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS +U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS +BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS +PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS +BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 9-Aug SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 11-Jul SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 11-Jul SUCCESS -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 21-Oct SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 7-Mar SUCCESS -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8-Aug SUCCESS +PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS +LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS +IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 11-Jul SUCCESS -MYCL GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2-Feb SUCCESS +ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS +MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 11-Jul SUCCESS +TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 20-Jan SUCCESS -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4-Apr SUCCESS -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 27-Oct SUCCESS -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 18-Jun SUCCESS -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 22-Mar SUCCESS -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 22-Mar SUCCESS -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 22-Mar SUCCESS -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 22-Mar SUCCESS -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 22-Mar SUCCESS -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 22-Mar SUCCESS +ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS +RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS +FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS +FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS +BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS +BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS +BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS +BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS +BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS +BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 21-Nov SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 15-Oct SUCCESS -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 17-Mar SUCCESS -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 11-Aug SUCCESS -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 7-Mar SUCCESS +FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS +AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS +BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS +NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 21-Feb SUCCESS +PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 16-Nov SUCCESS +PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 17-Apr SUCCESS -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 18-Mar SUCCESS +BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS +FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 3-Feb SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 17-Aug SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 21-Oct SUCCESS -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11-Nov SUCCESS +CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS +FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 11-Oct SUCCESS -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 11-Jun SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 11-Jul SUCCESS +TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS +TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 9-Jul SUCCESS +PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12-Dec SUCCESS -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 3-Jan SUCCESS +SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 27-Oct SUCCESS +FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 11-Jul SUCCESS -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 20-Aug SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 11-Aug SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS +MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 6-Mar SUCCESS +KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 16-Mar SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 17-Aug SUCCESS +EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS +FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS From cc508ca84f247d593b8b6df3fedd7d523bfa8118 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sun, 21 Mar 2021 20:27:32 -0400 Subject: [PATCH 36/68] With Entrez_IDs --- ...ata_mutations_extended_100.out.uniprot.txt | 198 +++++++++--------- 1 file changed, 99 insertions(+), 99 deletions(-) diff --git a/test/data/data_mutations_extended_100.out.uniprot.txt b/test/data/data_mutations_extended_100.out.uniprot.txt index 3129e08a..56501597 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS +ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 29-Jul SUCCESS +PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5-May SUCCESS +MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS +FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS +FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 30-Nov SUCCESS +NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS +NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 30-Apr SUCCESS +MLL3 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +MLL2 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 11-Feb SUCCESS +AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 15-Apr SUCCESS +TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg Nov-42 SUCCESS +RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 10-May SUCCESS +NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa Mar-33 SUCCESS +TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 11-May SUCCESS +ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 21-Oct SUCCESS +ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8-Aug SUCCESS +CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 8-May SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 11-Jul SUCCESS +RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 10-May SUCCESS +GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 6-May SUCCESS +LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 7-Apr SUCCESS +LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 7-Jan SUCCESS +U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 8-Jul SUCCESS +BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 17-Nov SUCCESS +LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 8-Jun SUCCESS +CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 15-Mar SUCCESS +PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 9-May SUCCESS +BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 15-Oct SUCCESS +ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS +PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 9-Aug SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 11-Jul SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 11-Jul SUCCESS +PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 21-Oct SUCCESS +LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 7-Mar SUCCESS +IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8-Aug SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS +ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 11-Jul SUCCESS +MYCL1 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2-Feb SUCCESS +POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS +TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 11-Jul SUCCESS +NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS +ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 20-Jan SUCCESS +RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4-Apr SUCCESS +FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 27-Oct SUCCESS +FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 18-Jun SUCCESS +BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 22-Mar SUCCESS +BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 22-Mar SUCCESS +BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 22-Mar SUCCESS +BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 22-Mar SUCCESS +BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 22-Mar SUCCESS +BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 22-Mar SUCCESS +CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS +KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 21-Nov SUCCESS +AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 15-Oct SUCCESS +BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 17-Mar SUCCESS +TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 11-Aug SUCCESS +NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 7-Mar SUCCESS +ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS +PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 21-Feb SUCCESS +NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS +PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 16-Nov SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 17-Apr SUCCESS +FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 18-Mar SUCCESS +NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS +CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 3-Feb SUCCESS +FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 17-Aug SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 21-Oct SUCCESS +BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11-Nov SUCCESS +MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS +NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS +TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 11-Oct SUCCESS +TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 11-Jun SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 11-Jul SUCCESS +PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS +PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 9-Jul SUCCESS +BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS +SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12-Dec SUCCESS +MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 3-Jan SUCCESS +PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS +FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 27-Oct SUCCESS +SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 11-Jul SUCCESS +EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 20-Aug SUCCESS +MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 11-Aug SUCCESS +IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS +KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 6-Mar SUCCESS +KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 16-Mar SUCCESS +FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 17-Aug SUCCESS +FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS +FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS From 6f1efba79670525816b2c60fa8742e4fda3601cf Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sun, 21 Mar 2021 20:31:32 -0400 Subject: [PATCH 37/68] Update data_mutations_extended_100.out.uniprot.txt --- ...ata_mutations_extended_100.out.uniprot.txt | 142 +++++++++--------- 1 file changed, 71 insertions(+), 71 deletions(-) diff --git a/test/data/data_mutations_extended_100.out.uniprot.txt b/test/data/data_mutations_extended_100.out.uniprot.txt index 56501597..a58c2446 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.txt @@ -2,101 +2,101 @@ #isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 29-Jul SUCCESS -PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5-May SUCCESS +ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS +PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 30-Nov SUCCESS +FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 30-Apr SUCCESS -MLL3 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -MLL2 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 11-Feb SUCCESS -AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 15-Apr SUCCESS -TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg Nov-42 SUCCESS -RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 10-May SUCCESS -NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa Mar-33 SUCCESS -TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 11-May SUCCESS +NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS +KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS +AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS +TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS +RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS +NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS +TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 21-Oct SUCCESS -ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8-Aug SUCCESS -CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 8-May SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 11-Jul SUCCESS -RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 10-May SUCCESS -GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 6-May SUCCESS -LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 7-Apr SUCCESS -LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 7-Jan SUCCESS -U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 8-Jul SUCCESS -BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 17-Nov SUCCESS -LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 8-Jun SUCCESS -CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 15-Mar SUCCESS -PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 9-May SUCCESS -BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 15-Oct SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS +CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS +GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS +LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS +U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS +BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS +PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS +BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 9-Aug SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 11-Jul SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 11-Jul SUCCESS -PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 21-Oct SUCCESS -LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 7-Mar SUCCESS -IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8-Aug SUCCESS +PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS +LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS +IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 11-Jul SUCCESS -MYCL1 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2-Feb SUCCESS +ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS +MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 11-Jul SUCCESS +TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 20-Jan SUCCESS -RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4-Apr SUCCESS -FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 27-Oct SUCCESS -FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 18-Jun SUCCESS -BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 22-Mar SUCCESS -BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 22-Mar SUCCESS -BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 22-Mar SUCCESS -BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 22-Mar SUCCESS -BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 22-Mar SUCCESS -BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 22-Mar SUCCESS +ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS +RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS +FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS +FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS +BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS +BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS +BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS +BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS +BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS +BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 21-Nov SUCCESS -AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 15-Oct SUCCESS -BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 17-Mar SUCCESS -TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 11-Aug SUCCESS -NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 7-Mar SUCCESS +FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS +AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS +BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS +NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 21-Feb SUCCESS +PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 16-Nov SUCCESS +PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 17-Apr SUCCESS -FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 18-Mar SUCCESS +BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS +FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 3-Feb SUCCESS -FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 17-Aug SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 21-Oct SUCCESS -BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11-Nov SUCCESS +CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS +FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 11-Oct SUCCESS -TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 11-Jun SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 11-Jul SUCCESS +TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS +TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 9-Jul SUCCESS +PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12-Dec SUCCESS -MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 3-Jan SUCCESS +SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 27-Oct SUCCESS +FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 11-Jul SUCCESS -EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 20-Aug SUCCESS -MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 11-Aug SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS +MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 6-Mar SUCCESS +KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 16-Mar SUCCESS -FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 17-Aug SUCCESS +EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS +FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS From 347c575e986963547cbebacdcc0cb542d1b10cc7 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sun, 21 Mar 2021 20:39:29 -0400 Subject: [PATCH 38/68] Update data_mutations_extended_100.out.uniprot.txt --- ...ata_mutations_extended_100.out.uniprot.txt | 200 +++++++++--------- 1 file changed, 100 insertions(+), 100 deletions(-) diff --git a/test/data/data_mutations_extended_100.out.uniprot.txt b/test/data/data_mutations_extended_100.out.uniprot.txt index a8482108..a58c2446 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS +ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS +PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS +MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS +FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS +FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS +NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS +NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS +KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS +AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS +TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS +RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS +NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS +TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS +ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS +CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS +GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS +LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS +U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS +BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS +PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS +BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS +ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS +PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS +LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS +IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS +ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS +MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS +POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS +TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS +NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS +ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS +RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS +FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS +FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS +BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS +BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS +BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS +BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS +BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS +BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS +CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS +KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS +AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS +BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS +NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS +ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS +PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS +NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS +PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS +FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS +NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS +CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS +FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS +MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS +NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS +TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS +TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS +PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS +BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS +SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS +PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS +FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS +SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS +MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS +IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS +KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS +KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS +FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS +FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS +FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS From 2c07a4d385f0caae47e0f0c482241714dbbb0358 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Sun, 21 Mar 2021 20:46:44 -0400 Subject: [PATCH 39/68] Update data_mutations_extended_100.out.uniprot.txt --- ...ata_mutations_extended_100.out.uniprot.txt | 198 +++++++++--------- 1 file changed, 99 insertions(+), 99 deletions(-) diff --git a/test/data/data_mutations_extended_100.out.uniprot.txt b/test/data/data_mutations_extended_100.out.uniprot.txt index a58c2446..3129e08a 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS -AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS -POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS -MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS -IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS +ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS +PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS +MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS +FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS +FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS +NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS +NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS +MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS +AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS +TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS +RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS +NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS +TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS +ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS +CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS +GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS +LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS +U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS +BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS +PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS +BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS +ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS +PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS +LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS +IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS +ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS +MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS +POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS +TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS +NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS +ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS +RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS +FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS +FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS +BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS +BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS +BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS +BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS +BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS +BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS +CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS +KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS +AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS +BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS +NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS +ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS +PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS +NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS +PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS +FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS +NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS +CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS +FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS +MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS +NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS +TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS +TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS +PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS +BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS +SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS +PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS +FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS +SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS +MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS +IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS +KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS +KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS +FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS +FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS +FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS From bb489aebb5ad2b5f463573ea932730a034ac3dc2 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Mon, 22 Mar 2021 14:07:25 -0400 Subject: [PATCH 40/68] Update data_mutations_extended_100.out.mskcc.txt --- .../data_mutations_extended_100.out.mskcc.txt | 198 +++++++++--------- 1 file changed, 99 insertions(+), 99 deletions(-) diff --git a/test/data/data_mutations_extended_100.out.mskcc.txt b/test/data/data_mutations_extended_100.out.mskcc.txt index 74bb5c33..86517142 100644 --- a/test/data/data_mutations_extended_100.out.mskcc.txt +++ b/test/data/data_mutations_extended_100.out.mskcc.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: mskcc Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000298171.2:c.154C>A p.Pro52Thr p.P52T ENST00000298171 NM_000369.2 52 Ccc/Acc 1/10 SUCCESS -AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000274335.5:c.1746-8_1748del p.X582_splice ENST00000274335 582 13/15 SUCCESS -PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000397332.2:c.851T>G p.Ile284Ser p.I284S ENST00000397332 NM_001033082.2 284 aTt/aGt 3/3 SUCCESS -POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000274335.5:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000274335 446 -/A 10/15 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 A A CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000320356.2:c.848C>T p.Thr283Met p.T283M ENST00000320356 NM_004456.4 283 aCg/aTg 8/20 SUCCESS -MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS -IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS +ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS +PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS +MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS +FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS +FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS +NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS +NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS +MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000298171.2:c.154C>A p.Pro52Thr p.P52T ENST00000298171 NM_000369.2 52 Ccc/Acc 1/10 SUCCESS +AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS +TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS +RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS +NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS +TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS +ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS +CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS +GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS +LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS +U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS +BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS +PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS +BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS +ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000274335.5:c.1746-8_1748del p.X582_splice ENST00000274335 582 13/15 SUCCESS +PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS +LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS +IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS +ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS +MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000397332.2:c.851T>G p.Ile284Ser p.I284S ENST00000397332 NM_001033082.2 284 aTt/aGt 3/3 SUCCESS +POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS +TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS +NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS +ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS +RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS +FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS +FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS +BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS +BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS +BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS +BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS +BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS +BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS +CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS +KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS +AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS +BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS +NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS +ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS +PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS +NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS +PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000274335.5:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000274335 446 -/A 10/15 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS +FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS +NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS +CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS +FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS +MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS +NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS +TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS +TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS +PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS +BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS +SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS +PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS +FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS +SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000320356.2:c.848C>T p.Thr283Met p.T283M ENST00000320356 NM_004456.4 283 aCg/aTg 8/20 SUCCESS +MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS +IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS +KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS +KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS +EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS +FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS +FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS +FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS From 2cb3c9e7555dc2b5540475bf4f5768ef301b03d3 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Mon, 22 Mar 2021 14:14:42 -0400 Subject: [PATCH 41/68] Update data_mutations_extended_100.out.uniprot.nucleotide_context.txt --- ...ded_100.out.uniprot.nucleotide_context.txt | 200 +++++++++--------- 1 file changed, 100 insertions(+), 100 deletions(-) diff --git a/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt b/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt index a69cb18e..b4c51dc5 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS -AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS -POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 A A CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS -MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS -IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 SUCCESS -EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Ref_Tri Var_Tri Annotation_Status +SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 CAT CTT SUCCESS +ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 CAC CGC SUCCESS +PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 GGC GAC SUCCESS +MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 TCT TGT SUCCESS +FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 CCG CAG SUCCESS +FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 GTG GCG SUCCESS +NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 CCG CTG SUCCESS +NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 CGA CAA SUCCESS +MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 GCA GTA SUCCESS +MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 CGG CAG SUCCESS +TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 GCC GAC SUCCESS +AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 TCC TTC SUCCESS +TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 CGG CAG SUCCESS +RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 CGG CAG SUCCESS +NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 TCG TTG SUCCESS +TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS +ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 GCC GTC SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS +ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 CTC CAC SUCCESS +CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 TCC TGC SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS +RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 CCA CGA SUCCESS +GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 GTC GAC SUCCESS +LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 CGA CAA SUCCESS +U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 GTT GCT SUCCESS +BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 TCT TAT SUCCESS +PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 ACG AGG SUCCESS +BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 ATT ACT SUCCESS +ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS +PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS +PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 GCA GAA SUCCESS +LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 GGG GCG SUCCESS +IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 CGC CAC SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 AGG AAG SUCCESS +CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 TAT TGT SUCCESS +ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 TGC TAC SUCCESS +MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 AAT ACT SUCCESS +POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 GGT GCT SUCCESS +TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 GCC GAC SUCCESS +NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 AGA ATA SUCCESS +ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 TCA TGA SUCCESS +RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 TCA TGA SUCCESS +FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 CGA CAA SUCCESS +FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 AGA ACA SUCCESS +BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 TCA TTA SUCCESS +BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 TCA TTA SUCCESS +BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 TCA TAA SUCCESS +BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 TCT TGT SUCCESS +BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 TCA TGA SUCCESS +BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 TCA TGA SUCCESS +CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 CGT CAT SUCCESS +KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 CTT CCT SUCCESS +AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 ATA ACA SUCCESS +BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 ACG ATG SUCCESS +NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 TCA TTA SUCCESS +ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 AGA AAA SUCCESS +PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 AGA AAA SUCCESS +NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 TCC TTC SUCCESS +PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 AGG AAG SUCCESS +BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 CGC CAC SUCCESS +FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 GGC GTC SUCCESS +NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 GTA GCA SUCCESS +CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 GGA GTA SUCCESS +FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS +BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 TGT TCT SUCCESS +MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 TCT TTT SUCCESS +NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 TCG TGG SUCCESS +TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 CGG CAG SUCCESS +TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 GAT GGT SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS +PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 CAT CGT SUCCESS +PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 GTT GCT SUCCESS +BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 AGG AAG SUCCESS +SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS +PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 TGG TCG SUCCESS +FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 TCA TGA SUCCESS +SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 GCG GGG SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS +EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 CGT CAT SUCCESS +MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 GAG GTG SUCCESS +IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 ATT AGT SUCCESS +KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 AGA ACA SUCCESS +KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 GGA GCA SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 AGG AAG SUCCESS +EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 CCA CTA SUCCESS +FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 TCC TTC SUCCESS +FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 TCA TGA SUCCESS +FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 TCT TGT SUCCESS From 9eda06eee0b7fc86c14ccb88b8c05c773360a3b4 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 11:53:17 -0400 Subject: [PATCH 42/68] Update MutationRecord.java --- .../java/org/cbioportal/models/MutationRecord.java | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/annotator/src/main/java/org/cbioportal/models/MutationRecord.java b/annotator/src/main/java/org/cbioportal/models/MutationRecord.java index 89751fcb..40ea121d 100644 --- a/annotator/src/main/java/org/cbioportal/models/MutationRecord.java +++ b/annotator/src/main/java/org/cbioportal/models/MutationRecord.java @@ -585,11 +585,11 @@ public void initHeader() { header.add("t_alt_count"); header.add("n_ref_count"); header.add("n_alt_count"); - header.add("GN_Immutable_Chromosome"); - header.add("GN_Immutable_Start_Position"); - header.add("GN_Immutable_End_Position"); - header.add("GN_Immutable_Reference_Allele"); - header.add("GN_Immutable_Tumor_Seq_Allele1"); - header.add("GN_Immutable_Tumor_Seq_Allele2"); + header.add("IGNORE_Genome_Nexus_Original_Chromosome"); + header.add("IGNORE_Genome_Nexus_Original_Start_Position"); + header.add("IGNORE_Genome_Nexus_Original_End_Position"); + header.add("IGNORE_Genome_Nexus_Original_Reference_Allele"); + header.add("IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1"); + header.add("IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2"); } } From 1796a33774b61f0ece6d9157795602aa4228127e Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 11:54:27 -0400 Subject: [PATCH 43/68] Update corner_cases.out.uniprot.txt --- test/data/corner_cases.out.uniprot.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/data/corner_cases.out.uniprot.txt b/test/data/corner_cases.out.uniprot.txt index 472c96c9..74b67ea9 100644 --- a/test/data/corner_cases.out.uniprot.txt +++ b/test/data/corner_cases.out.uniprot.txt @@ -1,5 +1,5 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - 7 116411872 116411900 TAACAAGCTCTTTCTTTCTCTCTGTTTTA - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 8 17796382 17796383 AC GT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS From c1a6893d80b1bac9faa88a55503e0c0aa77746a6 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 11:55:40 -0400 Subject: [PATCH 44/68] Rename GN_Immutable Columns --- test/data/corner_cases.out.mskcc.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/data/corner_cases.out.mskcc.txt b/test/data/corner_cases.out.mskcc.txt index 6b988dbd..f0e9c4f3 100644 --- a/test/data/corner_cases.out.mskcc.txt +++ b/test/data/corner_cases.out.mskcc.txt @@ -1,5 +1,5 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - 7 116411872 116411900 TAACAAGCTCTTTCTTTCTCTCTGTTTTA - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 8 17796382 17796383 AC GT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS From 9b2c7f6d2c64b1236812fac69d4aceb6a1b71f90 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 11:57:15 -0400 Subject: [PATCH 45/68] Rename GN_Immutable --- test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt b/test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt index 00fa8c00..a56f0286 100644 --- a/test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt +++ b/test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A 8 17796382 17796383 AC AAC GT ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 12 49435045 49435045 G C - ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 8 17796381 17796383 AAC AAC AGT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS From 9368fb93270747de6c0b12e96d67b8825c50842c Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 11:57:38 -0400 Subject: [PATCH 46/68] Rename GN_Immutable From e49285b46f8cdcaee5c2f09daef212ef4cd4e37e Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 11:58:21 -0400 Subject: [PATCH 47/68] Rename GN_Immutable Columns From 5d3ce001eb27103b6b816ef8b0750e675a88d287 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 11:58:57 -0400 Subject: [PATCH 48/68] Rename GN_Immutable Columns --- test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt b/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt index 663f7478..2f853bcf 100644 --- a/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt +++ b/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A 8 17796382 17796383 AC AAC GT ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 12 49435045 49435045 G C - ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 8 17796381 17796383 AAC AAC AGT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS From 7aec1d67ffdc8fc0ac01a9c6782663ce62b62599 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 11:59:25 -0400 Subject: [PATCH 49/68] Rename GN_Immutable Columns --- test/data/data_mutations_extended_100.out.mskcc.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/data/data_mutations_extended_100.out.mskcc.txt b/test/data/data_mutations_extended_100.out.mskcc.txt index 86517142..99f8e662 100644 --- a/test/data/data_mutations_extended_100.out.mskcc.txt +++ b/test/data/data_mutations_extended_100.out.mskcc.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS From 2c95b7eccf18585c724a25a88c0e6820b7314d15 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 11:59:47 -0400 Subject: [PATCH 50/68] Rename GN_Immutable Columns --- ...ta_mutations_extended_100.out.uniprot.nucleotide_context.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt b/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt index b4c51dc5..e699a865 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Ref_Tri Var_Tri Annotation_Status +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Ref_Tri Var_Tri Annotation_Status SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 CAT CTT SUCCESS ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 CAC CGC SUCCESS PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 GGC GAC SUCCESS From b515855727f9e414843390e342e77e8a3d53dd09 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 12:00:44 -0400 Subject: [PATCH 51/68] Rename GN_Immutable Columns --- test/data/data_mutations_extended_100.out.uniprot.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/data/data_mutations_extended_100.out.uniprot.txt b/test/data/data_mutations_extended_100.out.uniprot.txt index 3129e08a..ec6bcb38 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS From 302acb9b774641563fd20925856f9980850f9a4f Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 12:01:09 -0400 Subject: [PATCH 52/68] Rename GN_Immutable Columns --- test/data/minimal_example.out.uniprot.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/data/minimal_example.out.uniprot.txt b/test/data/minimal_example.out.uniprot.txt index e7f56cc9..11ed8c2b 100644 --- a/test/data/minimal_example.out.uniprot.txt +++ b/test/data/minimal_example.out.uniprot.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G 3 178916927 178916939 TAGGCAACCGTGA G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T 7 55220240 55220240 G T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 SUCCESS EGFR 1956 GRCh37 7 55242468 55242486 + protein_altering_variant In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA 7 55242467 55242486 AATTAAGAGAAGCAACATCT AGCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 SUCCESS From 5684276f3410142f826e548f129bc7f2fb0fa4d7 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 12:01:30 -0400 Subject: [PATCH 53/68] Rename GN_Immutable Columns --- test/data/my_variant_info_corner_cases.out.uniprot.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/data/my_variant_info_corner_cases.out.uniprot.txt b/test/data/my_variant_info_corner_cases.out.uniprot.txt index 74a3cf6a..02a735db 100644 --- a/test/data/my_variant_info_corner_cases.out.uniprot.txt +++ b/test/data/my_variant_info_corner_cases.out.uniprot.txt @@ -1,4 +1,4 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status BARD1 580 GRCh37 2 215645503 215645523 + inframe_deletion In_Frame_Del DEL TGGTGAAGAACATTCAGGCAA - - rs28997575 2 215645503 215645523 TGGTGAAGAACATTCAGGCAA - ENST00000260947.4:c.1075_1095del p.Leu359_Pro365del p.L359_P365del ENST00000260947 NM_000465.2 359 TTGCCTGAATGTTCTTCACCA/- 4/11 SUCCESS From f85d37c4ba27ea8a58dc1472fb7ccc3cf8b14482 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 12:26:21 -0400 Subject: [PATCH 54/68] Renamed GN_Immutable to Ignore_Genome_Nexus_Original --- .../cbioportal/models/AnnotatedRecord.java | 36 +++++++++---------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java b/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java index 3605cea1..74d2ecbe 100644 --- a/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java +++ b/annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java @@ -105,12 +105,12 @@ public AnnotatedRecord(String hugoSymbol, String tAltCount, String nRefCount, String nAltCount, - String GN_Immutable_Chromosome, - String GN_Immutable_Start_Position, - String GN_Immutable_End_Position, - String GN_Immutable_Reference_Allele, - String GN_Immutable_Tumor_Seq_Allele1, - String GN_Immutable_Tumor_Seq_Allele2, + String IGNORE_Genome_Nexus_Original_Chromosome, + String IGNORE_Genome_Nexus_Original_Start_Position, + String IGNORE_Genome_Nexus_Original_End_Position, + String IGNORE_Genome_Nexus_Original_Reference_Allele, + String IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1, + String IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2, String hgvsc, String hgvsp, String hgvspShort, @@ -163,12 +163,12 @@ public AnnotatedRecord(String hugoSymbol, tAltCount, nRefCount, nAltCount, - GN_Immutable_Chromosome, - GN_Immutable_Start_Position, - GN_Immutable_End_Position, - GN_Immutable_Reference_Allele, - GN_Immutable_Tumor_Seq_Allele1, - GN_Immutable_Tumor_Seq_Allele2, + IGNORE_Genome_Nexus_Original_Chromosome, + IGNORE_Genome_Nexus_Original_Start_Position, + IGNORE_Genome_Nexus_Original_End_Position, + IGNORE_Genome_Nexus_Original_Reference_Allele, + IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1, + IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2, additionalProperties); this.hgvsc = hgvsc; this.hgvsp = hgvsp; @@ -225,12 +225,12 @@ public AnnotatedRecord(MutationRecord mRecord) { this.tAltCount = mRecord.getT_ALT_COUNT(); this.nRefCount = mRecord.getN_REF_COUNT(); this.nAltCount = mRecord.getN_ALT_COUNT(); - this.GN_Immutable_Chromosome = mRecord.getGN_IMMUTABLE_CHROMOSOME(); - this.GN_Immutable_Start_Position = mRecord.getGN_IMMUTABLE_START_POSITION(); - this.GN_Immutable_End_Position = mRecord.getGN_IMMUTABLE_END_POSITION(); - this.GN_Immutable_Reference_Allele = mRecord.getGN_IMMUTABLE_REFERENCE_ALLELE(); - this.GN_Immutable_Tumor_Seq_Allele1 = mRecord.getGN_IMMUTABLE_TUMOR_SEQ_ALLELE1(); - this.GN_Immutable_Tumor_Seq_Allele2 = mRecord.getGN_IMMUTABLE_TUMOR_SEQ_ALLELE2(); + this.IGNORE_Genome_Nexus_Original_Chromosome = mRecord.getIGNORE_GENOME_NEXUS_ORIGINAL_CHROMOSOME(); + this.IGNORE_Genome_Nexus_Original_Start_Position = mRecord.getIGNORE_GENOME_NEXUS_ORIGINAL_START_POSITION(); + this.IGNORE_Genome_Nexus_Original_End_Position = mRecord.getIGNORE_GENOME_NEXUS_ORIGINAL_END_POSITION(); + this.IGNORE_Genome_Nexus_Original_Reference_Allele = mRecord.getIGNORE_GENOME_NEXUS_ORIGINAL_REFERENCE_ALLELE(); + this.IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 = mRecord.getIGNORE_GENOME_NEXUS_ORIGINAL_TUMOR_SEQ_ALLELE1(); + this.IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 = mRecord.getIGNORE_GENOME_NEXUS_ORIGINAL_TUMOR_SEQ_ALLELE2(); this.hgvsc = additionalProperties.get("HGVSc") != null ? additionalProperties.get("HGVSc") : ""; this.hgvsp = additionalProperties.get("HGVSp") != null ? additionalProperties.get("HGVSp") : ""; this.hgvspShort = additionalProperties.get("HGVSp_Short"); From b52e139b96b82a1c51d7f5488f2aa5c274772352 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 12:27:03 -0400 Subject: [PATCH 55/68] Renamed GN_Immutable to Ignore_Genome_Nexus_Original --- .../org/cbioportal/models/MutationRecord.java | 78 +++++++++---------- 1 file changed, 39 insertions(+), 39 deletions(-) diff --git a/annotator/src/main/java/org/cbioportal/models/MutationRecord.java b/annotator/src/main/java/org/cbioportal/models/MutationRecord.java index 40ea121d..1b4ce1fb 100644 --- a/annotator/src/main/java/org/cbioportal/models/MutationRecord.java +++ b/annotator/src/main/java/org/cbioportal/models/MutationRecord.java @@ -77,12 +77,12 @@ public class MutationRecord { protected String tAltCount; protected String nRefCount; protected String nAltCount; - protected String GN_Immutable_Chromosome; - protected String GN_Immutable_Start_Position; - protected String GN_Immutable_End_Position; - protected String GN_Immutable_Reference_Allele; - protected String GN_Immutable_Tumor_Seq_Allele1; - protected String GN_Immutable_Tumor_Seq_Allele2; + protected String IGNORE_Genome_Nexus_Original_Chromosome; + protected String IGNORE_Genome_Nexus_Original_Start_Position; + protected String IGNORE_Genome_Nexus_Original_End_Position; + protected String IGNORE_Genome_Nexus_Original_Reference_Allele; + protected String IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1; + protected String IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2; protected Map additionalProperties = new LinkedHashMap<>(); protected List header = new ArrayList<>(); @@ -99,9 +99,9 @@ public MutationRecord(String hugoSymbol, String entrezGeneId, String center, Str String verificationStatus, String validationStatus, String mutationStatus, String sequencingPhase, String sequencingSource, String validationMethod, String score, String bamFile, String sequencer, String tumorSampleUUID, String matchedNormSampleUUID, String tRefCount, String tAltCount, - String nRefCount, String nAltCount, String GN_Immutable_Chromosome, String GN_Immutable_Start_Position, - String GN_Immutable_End_Position, String GN_Immutable_Reference_Allele, String GN_Immutable_Tumor_Seq_Allele1, - String GN_Immutable_Tumor_Seq_Allele2, Map additionalProperties) { + String nRefCount, String nAltCount, String IGNORE_Genome_Nexus_Original_Chromosome, String IGNORE_Genome_Nexus_Original_Start_Position, + String IGNORE_Genome_Nexus_Original_End_Position, String IGNORE_Genome_Nexus_Original_Reference_Allele, String IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1, + String IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2, Map additionalProperties) { this.hugoSymbol = hugoSymbol; this.entrezGeneId = entrezGeneId; @@ -141,12 +141,12 @@ public MutationRecord(String hugoSymbol, String entrezGeneId, String center, Str this.tAltCount = tAltCount; this.nRefCount = nRefCount; this.nAltCount = nAltCount; - this.GN_Immutable_Chromosome = GN_Immutable_Chromosome; - this.GN_Immutable_Start_Position = GN_Immutable_Start_Position; - this.GN_Immutable_End_Position = GN_Immutable_End_Position; - this.GN_Immutable_Reference_Allele = GN_Immutable_Reference_Allele; - this.GN_Immutable_Tumor_Seq_Allele1 = GN_Immutable_Tumor_Seq_Allele1; - this.GN_Immutable_Tumor_Seq_Allele2 = GN_Immutable_Tumor_Seq_Allele2; + this.IGNORE_Genome_Nexus_Original_Chromosome = IGNORE_Genome_Nexus_Original_Chromosome; + this.IGNORE_Genome_Nexus_Original_Start_Position = IGNORE_Genome_Nexus_Original_Start_Position; + this.IGNORE_Genome_Nexus_Original_End_Position = IGNORE_Genome_Nexus_Original_End_Position; + this.IGNORE_Genome_Nexus_Original_Reference_Allele = IGNORE_Genome_Nexus_Original_Reference_Allele; + this.IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 = IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1; + this.IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 = IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2; this.additionalProperties = additionalProperties; initHeader(); } @@ -455,52 +455,52 @@ public void setN_ALT_COUNT(String nAltCount) { this.nAltCount = nAltCount; } - public String getGN_IMMUTABLE_CHROMOSOME() { - return this.GN_Immutable_Chromosome == null ? "" : this.GN_Immutable_Chromosome; + public String getIGNORE_GENOME_NEXUS_ORIGINAL_CHROMOSOME() { + return this.IGNORE_Genome_Nexus_Original_Chromosome == null ? "" : this.IGNORE_Genome_Nexus_Original_Chromosome; } - public void setGN_IMMUTABLE_CHROMOSOME(String GN_Immutable_Chromosome) { - this.GN_Immutable_Chromosome = GN_Immutable_Chromosome; + public void setIGNORE_GENOME_NEXUS_ORIGINAL_CHROMOSOME(String IGNORE_Genome_Nexus_Original_Chromosome) { + this.IGNORE_Genome_Nexus_Original_Chromosome = IGNORE_Genome_Nexus_Original_Chromosome; } - public String getGN_IMMUTABLE_START_POSITION() { - return this.GN_Immutable_Start_Position == null ? "" : this.GN_Immutable_Start_Position; + public String getIGNORE_GENOME_NEXUS_ORIGINAL_START_POSITION() { + return this.IGNORE_Genome_Nexus_Original_Start_Position == null ? "" : this.IGNORE_Genome_Nexus_Original_Start_Position; } - public void setGN_IMMUTABLE_START_POSITION(String GN_Immutable_Start_Position) { - this.GN_Immutable_Start_Position = GN_Immutable_Start_Position; + public void setIGNORE_GENOME_NEXUS_ORIGINAL_START_POSITION(String IGNORE_Genome_Nexus_Original_Start_Position) { + this.IGNORE_Genome_Nexus_Original_Start_Position = IGNORE_Genome_Nexus_Original_Start_Position; } - public String getGN_IMMUTABLE_END_POSITION() { - return this.GN_Immutable_End_Position == null ? "" : this.GN_Immutable_End_Position; + public String getIGNORE_GENOME_NEXUS_ORIGINAL_END_POSITION() { + return this.IGNORE_Genome_Nexus_Original_End_Position == null ? "" : this.IGNORE_Genome_Nexus_Original_End_Position; } - public void setGN_IMMUTABLE_END_POSITION(String GN_Immutable_End_Position) { - this.GN_Immutable_End_Position = GN_Immutable_End_Position; + public void setIGNORE_GENOME_NEXUS_ORIGINAL_END_POSITION(String IGNORE_Genome_Nexus_Original_End_Position) { + this.IGNORE_Genome_Nexus_Original_End_Position = IGNORE_Genome_Nexus_Original_End_Position; } - public String getGN_IMMUTABLE_REFERENCE_ALLELE() { - return this.GN_Immutable_Reference_Allele == null ? "" : this.GN_Immutable_Reference_Allele; + public String getIGNORE_GENOME_NEXUS_ORIGINAL_REFERENCE_ALLELE() { + return this.IGNORE_Genome_Nexus_Original_Reference_Allele == null ? "" : this.IGNORE_Genome_Nexus_Original_Reference_Allele; } - public void setGN_IMMUTABLE_REFERENCE_ALLELE(String GN_Immutable_Reference_Allele) { - this.GN_Immutable_Reference_Allele = GN_Immutable_Reference_Allele; + public void setIGNORE_GENOME_NEXUS_ORIGINAL_REFERENCE_ALLELE(String IGNORE_Genome_Nexus_Original_Reference_Allele) { + this.IGNORE_Genome_Nexus_Original_Reference_Allele = IGNORE_Genome_Nexus_Original_Reference_Allele; } - public String getGN_IMMUTABLE_TUMOR_SEQ_ALLELE1() { - return this.GN_Immutable_Tumor_Seq_Allele1 == null ? "" : this.GN_Immutable_Tumor_Seq_Allele1; + public String getIGNORE_GENOME_NEXUS_ORIGINAL_TUMOR_SEQ_ALLELE1() { + return this.IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 == null ? "" : this.IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1; } - public void setGN_IMMUTABLE_TUMOR_SEQ_ALLELE1(String GN_Immutable_Tumor_Seq_Allele1) { - this.GN_Immutable_Tumor_Seq_Allele1 = GN_Immutable_Tumor_Seq_Allele1; + public void setIGNORE_GENOME_NEXUS_ORIGINAL_TUMOR_SEQ_ALLELE1(String IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1) { + this.IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 = IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1; } - public String getGN_IMMUTABLE_TUMOR_SEQ_ALLELE2() { - return this.GN_Immutable_Tumor_Seq_Allele2 == null ? "" : this.GN_Immutable_Tumor_Seq_Allele2; + public String getIGNORE_GENOME_NEXUS_ORIGINAL_TUMOR_SEQ_ALLELE2() { + return this.IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 == null ? "" : this.IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2; } - public void setGN_IMMUTABLE_TUMOR_SEQ_ALLELE2(String GN_Immutable_Tumor_Seq_Allele2) { - this.GN_Immutable_Tumor_Seq_Allele2 = GN_Immutable_Tumor_Seq_Allele2; + public void setIGNORE_GENOME_NEXUS_ORIGINAL_TUMOR_SEQ_ALLELE2(String IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2) { + this.IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 = IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2; } public void addAdditionalProperty(String property, String value) { From 5fa823c106e3d5e7913e1329cb75f536b55ea31b Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 12:27:32 -0400 Subject: [PATCH 56/68] Renamed GN_Immutable to Ignore_Genome_Nexus_Original --- .../annotator/internal/GenomeNexusImpl.java | 38 +++++++++---------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java index 94d4109d..703e9846 100644 --- a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java +++ b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java @@ -231,19 +231,19 @@ public AnnotatedRecord convertResponseToAnnotatedRecord(VariantAnnotation gnResp // variant attributes (pos,ref,alt1,alt2) to be mutable? } - String GN_Immutable_Chromosome_Value; - String GN_Immutable_Start_Position_Value; - String GN_Immutable_End_Position_Value; - String GN_Immutable_Reference_Allele_Value; - String GN_Immutable_Tumor_Seq_Allele1_Value; - String GN_Immutable_Tumor_Seq_Allele2_Value; - - GN_Immutable_Chromosome_Value = ((GN_Immutable_Chromosome_Value = mRecord.getGN_IMMUTABLE_CHROMOSOME()) != "") ? GN_Immutable_Chromosome_Value : mRecord.getCHROMOSOME(); - GN_Immutable_Start_Position_Value = ((GN_Immutable_Start_Position_Value = mRecord.getGN_IMMUTABLE_START_POSITION()) != "") ? GN_Immutable_Start_Position_Value : mRecord.getSTART_POSITION(); - GN_Immutable_End_Position_Value = ((GN_Immutable_End_Position_Value = mRecord.getGN_IMMUTABLE_END_POSITION()) != "") ? GN_Immutable_End_Position_Value : mRecord.getEND_POSITION(); - GN_Immutable_Reference_Allele_Value = ((GN_Immutable_Reference_Allele_Value = mRecord.getGN_IMMUTABLE_REFERENCE_ALLELE()) != "") ? GN_Immutable_Reference_Allele_Value : mRecord.getREFERENCE_ALLELE(); - GN_Immutable_Tumor_Seq_Allele1_Value = ((GN_Immutable_Tumor_Seq_Allele1_Value = mRecord.getGN_IMMUTABLE_TUMOR_SEQ_ALLELE1()) != "") ? GN_Immutable_Tumor_Seq_Allele1_Value : mRecord.getTUMOR_SEQ_ALLELE1(); - GN_Immutable_Tumor_Seq_Allele2_Value = ((GN_Immutable_Tumor_Seq_Allele2_Value = mRecord.getGN_IMMUTABLE_TUMOR_SEQ_ALLELE2()) != "") ? GN_Immutable_Tumor_Seq_Allele2_Value : mRecord.getTUMOR_SEQ_ALLELE2(); + String IGNORE_Genome_Nexus_Original_Chromosome_Value; + String IGNORE_Genome_Nexus_Original_Start_Position_Value; + String IGNORE_Genome_Nexus_Original_End_Position_Value; + String IGNORE_Genome_Nexus_Original_Reference_Allele_Value; + String IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1_Value; + String IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2_Value; + + IGNORE_Genome_Nexus_Original_Chromosome_Value = ((IGNORE_Genome_Nexus_Original_Chromosome_Value = mRecord.getIGNORE_GENOME_NEXUS_ORIGINAL_CHROMOSOME()) != "") ? IGNORE_Genome_Nexus_Original_Chromosome_Value : mRecord.getCHROMOSOME(); + IGNORE_Genome_Nexus_Original_Start_Position_Value = ((IGNORE_Genome_Nexus_Original_Start_Position_Value = mRecord.getIGNORE_GENOME_NEXUS_ORIGINAL_START_POSITION()) != "") ? IGNORE_Genome_Nexus_Original_Start_Position_Value : mRecord.getSTART_POSITION(); + IGNORE_Genome_Nexus_Original_End_Position_Value = ((IGNORE_Genome_Nexus_Original_End_Position_Value = mRecord.getIGNORE_GENOME_NEXUS_ORIGINAL_END_POSITION()) != "") ? IGNORE_Genome_Nexus_Original_End_Position_Value : mRecord.getEND_POSITION(); + IGNORE_Genome_Nexus_Original_Reference_Allele_Value = ((IGNORE_Genome_Nexus_Original_Reference_Allele_Value = mRecord.getIGNORE_GENOME_NEXUS_ORIGINAL_REFERENCE_ALLELE()) != "") ? IGNORE_Genome_Nexus_Original_Reference_Allele_Value : mRecord.getREFERENCE_ALLELE(); + IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1_Value = ((IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1_Value = mRecord.getIGNORE_GENOME_NEXUS_ORIGINAL_TUMOR_SEQ_ALLELE1()) != "") ? IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1_Value : mRecord.getTUMOR_SEQ_ALLELE1(); + IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2_Value = ((IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2_Value = mRecord.getIGNORE_GENOME_NEXUS_ORIGINAL_TUMOR_SEQ_ALLELE2()) != "") ? IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2_Value : mRecord.getTUMOR_SEQ_ALLELE2(); // annotate the record AnnotatedRecord annotatedRecord= new AnnotatedRecord(annotationUtil.resolveHugoSymbol(canonicalTranscript, mRecord, replace), @@ -284,12 +284,12 @@ public AnnotatedRecord convertResponseToAnnotatedRecord(VariantAnnotation gnResp mRecord.getT_ALT_COUNT(), mRecord.getN_REF_COUNT(), mRecord.getN_ALT_COUNT(), - GN_Immutable_Chromosome_Value, - GN_Immutable_Start_Position_Value, - GN_Immutable_End_Position_Value, - GN_Immutable_Reference_Allele_Value, - GN_Immutable_Tumor_Seq_Allele1_Value, - GN_Immutable_Tumor_Seq_Allele2_Value, + IGNORE_Genome_Nexus_Original_Chromosome_Value, + IGNORE_Genome_Nexus_Original_Start_Position_Value, + IGNORE_Genome_Nexus_Original_End_Position_Value, + IGNORE_Genome_Nexus_Original_Reference_Allele_Value, + IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1_Value, + IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2_Value, annotationUtil.resolveHgvsc(canonicalTranscript), annotationUtil.resolveHgvsp(canonicalTranscript), annotationUtil.resolveHgvspShort(canonicalTranscript), From a92175c0e20bd0343305ba23c1b9613a8d3c322c Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 12:29:23 -0400 Subject: [PATCH 57/68] Removed GN_Immutable Columns --- test/data/data_mutations_extended_100.in.txt | 200 +++++++++---------- 1 file changed, 100 insertions(+), 100 deletions(-) diff --git a/test/data/data_mutations_extended_100.in.txt b/test/data/data_mutations_extended_100.in.txt index 9b436574..941bce1e 100644 --- a/test/data/data_mutations_extended_100.in.txt +++ b/test/data/data_mutations_extended_100.in.txt @@ -1,100 +1,100 @@ -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count GN_Immutable_Chromosome GN_Immutable_Start_Position GN_Immutable_End_Position GN_Immutable_Reference_Allele GN_Immutable_Tumor_Seq_Allele1 GN_Immutable_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 1 16265908 16265908 A A T ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G P-0000004-T01-IM3 180 13 2 29543736 29543736 A A G ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 225 15 2 242793433 242793433 G G A ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G P-0000004-T01-IM3 370 12 5 56177843 56177843 C C G ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A P-0000004-T01-IM3 360 25 5 180030313 180030313 C C A ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C P-0000004-T01-IM3 273 22 5 180051003 180051003 T T C ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 279 17 6 32178570 32178570 C C T ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 207 11 6 32188823 32188823 G G A ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 7 151945083 151945083 C C T ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 247 16 12 49433883 49433883 G G A ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A P-0000004-T01-IM3 195 13 14 81422178 81422178 C C A ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 202 244 14 105246551 105246551 C C T ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 236 22 16 2110795 2110795 G G A ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 296 41 17 56440643 56440643 G G A ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 274 17 19 15303190 15303190 C C T ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 17 7578503 7578518 CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - ENST00000269305.4:c.412_427delGCCAAGACCTGCCCTG p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 2 29450535 29450535 C C T ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A P-0000015-T01-IM3 80 56 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 6 152419920 152419920 T T A ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 12 58144485 58144485 C C G ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A P-0000015-T01-IM3 131 61 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 17 56440637 56440637 C C G ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 10 8111513 8111514 - - G ENST00000346208.3:c.1003dupG p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 6 150001256 150001256 T T A ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A P-0000023-T01-IM3 511 38 6 150023076 150023076 G G A ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 21 44514647 44514647 T T C ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 3 52439259 52439259 G G - ENST00000460680.1:c.983delC p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 13 21555731 21555732 - - A ENST00000382592.4:c.2538dupT p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A P-0000024-T01-IM3 965 280 3 41266113 41266113 C C A ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G P-0000024-T01-IM3 846 231 10 89692904 89692904 C C G ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C P-0000024-T01-IM3 647 317 X 39921444 39921444 T T C ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 1 27105878 27105881 AGCT AGCT - ENST00000324856.7:c.5489_5492delAGCT p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 5 67591238 67591248 TGTTTTTCAGG TGTTTTTCAGG - ENST00000521381.1:c.1746-8_1748delTTTTTCAGGTG p.X582_splice ENST00000521381 NM_181523.2 -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A P-0000024-T01-IM3 170 53 10 89720720 89720721 - - A ENST00000371953.3:c.875dupA p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000025-T01-IM3 827 49 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000026-T01-IM3 261 370 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A P-0000026-T01-IM3 325 468 3 178936094 178936094 C C A ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 6 150004871 150004871 G G C ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 7 50467844 50467844 G G A ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000027-T01-IM3 122 16 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 2 225339012 225339012 A A G ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 9 133750275 133750275 G G A ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 1 40363378 40363378 A A C ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 12 133202730 133202730 G G C ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A P-0000037-T01-IM3 293 230 17 7577534 7577534 C C A ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 17 15960850 15960850 G G T ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 1 27023307 27023307 C C G ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 3 72427550 72427550 C C G ENST00000477973.2:c.938G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A P-0000034-T01-IM3 659 78 4 187540074 187540074 G G A ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 5 176518800 176518800 G G C ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 15 91292745 91292745 C C T ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T P-0000034-T01-IM3 631 51 15 91292809 91292809 C C T ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 15 91292815 91292815 C C A ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 15 91292904 91292904 C C G ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 15 91292951 91292951 C C G ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 15 91293024 91293024 C C G ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A P-0000034-T01-IM3 217 76 19 42796756 42796756 G G A ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 X 44969425 44969425 G G - ENST00000377967.4:c.4108delG p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 3 71090639 71090639 T T C ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C P-0000047-T01-IM3 220 25 14 105239862 105239862 T T C ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 3 52443574 52443592 GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - ENST00000460680.1:c.100_118delGACCTTCAGAGCAAATGTC p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 698 390 17 7577120 7577120 C C T ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 1 115256510 115256510 C C T ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 3 142231242 142231242 G G A ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 935 227 3 178916854 178916854 G G A ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 19 15281521 15281521 C C T ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 5 67589575 67589576 - - A ENST00000521381.1:c.1344dupA p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000056-T01-IM3 271 161 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A P-0000056-T01-IM3 617 328 3 52442579 52442579 G G A ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag -FGFR3 37 4 1806090 1806090 In_Frame_Ins DEL A A CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 6 32172007 32172007 C C G ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A P-0000057-T01-IM3 442 261 17 7574003 7574003 G G A ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G P-0000058-T01-IM3 156 348 17 7578265 7578265 A A G ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000060-T01-IM3 162 217 17 7577538 7577538 C C T ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G P-0000060-T01-IM3 779 359 3 178952085 178952085 A A G ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 10 89717618 89717618 T T C ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A P-0000060-T01-IM3 293 148 13 32945237 32945237 G G A ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 7 128851867 128851867 C C - ENST00000249373.3:c.1943delC p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 1 150551364 150551381 GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC ENST00000369026.2:c.626_643delCGCTGGAGACCTTACGACinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C P-0000061-T01-IM3 762 155 3 178952090 178952090 G G C ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 4 187539969 187539969 C C G ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 19 11144146 11144146 C C G ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A P-0000062-T01-IM3 265 581 17 7577539 7577539 G G A ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A P-0000062-T01-IM3 980 54 7 148523605 148523605 G G A ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 12 69222656 69222656 A A T ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 15 99486153 99486153 T T G ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 807 422 19 10602303 10602303 G G C ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 X 53223386 53223386 G G C ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000063-T01-IM3 18 79 5 1295228 1295228 G G A ENST00000310581 NM_198253.2 -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T P-0000063-T01-IM3 540 220 3 134670264 134670264 C C T ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 4 1806225 1806225 C C T ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 4 187518888 187518888 C C G ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 4 187518921 187518921 C C G ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons +SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt +ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg +PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc +MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt +FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg +FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg +NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg +NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg +MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA +MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg +TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc +AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag +TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg +RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg +NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa +TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427delGCCAAGACCTGCCCTG p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg +ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag +ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc +CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg +RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg +GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dupG p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G +LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc +LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga +U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc +BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983delC p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct +LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dupT p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T +CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt +PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga +BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt +ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492delAGCT p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at +PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748delTTTTTCAGGTG p.X582_splice ENST00000521381 NM_181523.2 +PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dupA p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg +PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag +LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct +IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 +CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat +ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc +MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt +POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG +TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT +NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att +ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa +RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.938G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat +FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga +FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat +BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag +BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa +BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa +BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc +BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG +BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac +CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg +KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108delG p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt +FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt +AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt +BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118delGACCTTCAGAGCAAATGTC p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag +TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt +NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA +ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt +PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa +NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag +PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dupA p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 +BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc +FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca +NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc +CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag +FGFR3 37 4 1806090 1806090 In_Frame_Ins DEL A A CACT P-0000056-T01-IM3 816 370 +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag +BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa +MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt +NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag +TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga +TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg +PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt +PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt +BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa +SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943delC p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc +MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delCGCTGGAGACCTTACGACinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg +PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt +FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac +SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg +EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg +MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg +IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG +KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG +KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 +EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag +FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc +FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac +FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat From 5412b18451863ab9bd3a0a30902ed0d1ca448604 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 12:29:44 -0400 Subject: [PATCH 58/68] Renamed GN_Immutable to Ignore_Genome_Nexus_Original --- test/data/data_mutations_extended_100.out.mskcc.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/data/data_mutations_extended_100.out.mskcc.txt b/test/data/data_mutations_extended_100.out.mskcc.txt index 99f8e662..75bf9ada 100644 --- a/test/data/data_mutations_extended_100.out.mskcc.txt +++ b/test/data/data_mutations_extended_100.out.mskcc.txt @@ -73,7 +73,7 @@ BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 A A CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS From c78e40de371c6049039f86a3f6c5d6838eade032 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 12:30:02 -0400 Subject: [PATCH 59/68] Renamed GN_Immutable to Ignore_Genome_Nexus_Original --- ...ta_mutations_extended_100.out.uniprot.nucleotide_context.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt b/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt index e699a865..0a182aa9 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt @@ -73,7 +73,7 @@ BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 GGC GTC SUCCESS NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 GTA GCA SUCCESS CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 GGA GTA SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 A A CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 TGT TCT SUCCESS MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 TCT TTT SUCCESS From 0007c9661d9411db03e5b90302ee64735c13f02c Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 12:30:20 -0400 Subject: [PATCH 60/68] Renamed GN_Immutable to Ignore_Genome_Nexus_Original --- test/data/data_mutations_extended_100.out.uniprot.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/data/data_mutations_extended_100.out.uniprot.txt b/test/data/data_mutations_extended_100.out.uniprot.txt index ec6bcb38..12cf99ca 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.txt @@ -73,7 +73,7 @@ BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 5 176517519 176517519 G G T ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 6 32170183 32170183 T T C ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 6 36652074 36652074 G G T ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 G G CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 4 1806090 1806090 A A CACT ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 3 178936091 178936091 G G A ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 2 215593578 215593578 G G C ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 3 185198238 185198238 C C T ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS From b8a5a5aed0e5824e5046fe3b48e72fdd67fedb53 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 15:48:38 -0400 Subject: [PATCH 61/68] Add files via upload --- test/data/immutable_columns_test.in.txt | 6 ++++++ test/data/immutable_columns_test.out.uniprot.txt | 6 ++++++ 2 files changed, 12 insertions(+) create mode 100644 test/data/immutable_columns_test.in.txt create mode 100644 test/data/immutable_columns_test.out.uniprot.txt diff --git a/test/data/immutable_columns_test.in.txt b/test/data/immutable_columns_test.in.txt new file mode 100644 index 00000000..11ed8c2b --- /dev/null +++ b/test/data/immutable_columns_test.in.txt @@ -0,0 +1,6 @@ +#genome_nexus_version: 0-unknown-version-SNAPSHOT +#isoform: uniprot +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G 3 178916927 178916939 TAGGCAACCGTGA G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS +EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T 7 55220240 55220240 G T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 SUCCESS +EGFR 1956 GRCh37 7 55242468 55242486 + protein_altering_variant In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA 7 55242467 55242486 AATTAAGAGAAGCAACATCT AGCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 SUCCESS diff --git a/test/data/immutable_columns_test.out.uniprot.txt b/test/data/immutable_columns_test.out.uniprot.txt new file mode 100644 index 00000000..a7c553e4 --- /dev/null +++ b/test/data/immutable_columns_test.out.uniprot.txt @@ -0,0 +1,6 @@ +#genome_nexus_version: 0-unknown-version-SNAPSHOT +#isoform: uniprot +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status +PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G 3 178916927 178916939 TAGGCAACCGTGA G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS +EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T 7 55220240 55220240 G T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 SUCCESS +EGFR 1956 GRCh37 7 55242469 55242486 + frameshift_variant Frame_Shift_Del DEL TTAAGAGAAGCAACATCT AGCAA GCAA 7 55242467 55242486 AATTAAGAGAAGCAACATCT AGCAA ENST00000275493.2:c.2239_2256delinsGCAA p.Leu747AlafsTer11 p.L747Afs*11 ENST00000275493 NM_005228.3 747 TTAAGAGAAGCAACATCT/GCAA 19/28 SUCCESS From 5b0b1a4a067962b9357b4e74af9fe924249cb54f Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 16:03:24 -0400 Subject: [PATCH 62/68] Update config.yml --- .circleci/config.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 1c643606..88e86a9a 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -91,9 +91,13 @@ jobs: command: 'java -Dgenomenexus.enrichment_fields=annotation_summary,my_variant_info -jar annotationPipeline/target/annotationPipeline-*.jar -r --filename test/data/my_variant_info_corner_cases.in.txt --output-filename test/data/my_variant_info_corner_cases.out.uniprot.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/my_variant_info_corner_cases.out.uniprot.txt || (echo simple MAF uniprot output changed test/data/my_variant_info_corner_cases.out.uniprot.txt)' - run: - name: "check if nucleotide_context provides Ref_Tri and Var_Tri columnsj" + name: "check if nucleotide_context provides Ref_Tri and Var_Tri columns" command: 'java -Dgenomenexus.enrichment_fields=annotation_summary,nucleotide_context -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/data_mutations_extended_100.in.txt --output-filename test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt || (echo simple MAF uniprot output changed test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt)' + - run: + name: "check if columns prefixed with IGNORE_Genome_Nexus_Original_ are immutable" + command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar -r --filename test/data/immutable_columns_test.in.txt --output-filename test/data/immutable_columns_test.out.uniprot.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/immutable_columns_test.out.uniprot.txt || (echo simple MAF uniprot output changed test/data/immutable_columns_test.out.uniprot.txt && exit 1)' + - store_artifacts: path: test/data destination: /test-data-output From 3011b969d5758caae1fa9fec05a0a49a2a044fed Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 16:09:29 -0400 Subject: [PATCH 63/68] Reverted to Old Version --- .circleci/config.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 88e86a9a..1c643606 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -91,13 +91,9 @@ jobs: command: 'java -Dgenomenexus.enrichment_fields=annotation_summary,my_variant_info -jar annotationPipeline/target/annotationPipeline-*.jar -r --filename test/data/my_variant_info_corner_cases.in.txt --output-filename test/data/my_variant_info_corner_cases.out.uniprot.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/my_variant_info_corner_cases.out.uniprot.txt || (echo simple MAF uniprot output changed test/data/my_variant_info_corner_cases.out.uniprot.txt)' - run: - name: "check if nucleotide_context provides Ref_Tri and Var_Tri columns" + name: "check if nucleotide_context provides Ref_Tri and Var_Tri columnsj" command: 'java -Dgenomenexus.enrichment_fields=annotation_summary,nucleotide_context -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/data_mutations_extended_100.in.txt --output-filename test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt || (echo simple MAF uniprot output changed test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt)' - - run: - name: "check if columns prefixed with IGNORE_Genome_Nexus_Original_ are immutable" - command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar -r --filename test/data/immutable_columns_test.in.txt --output-filename test/data/immutable_columns_test.out.uniprot.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/immutable_columns_test.out.uniprot.txt || (echo simple MAF uniprot output changed test/data/immutable_columns_test.out.uniprot.txt && exit 1)' - - store_artifacts: path: test/data destination: /test-data-output From 14ceeba73180ebe3cb513ec2c6fe985d797b2bb4 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 16:18:07 -0400 Subject: [PATCH 64/68] Renamed GN_Immutable to IGNORE_Genome_Nexus_Original From b74685ffa4a964291e01caebb524a5095dcec9bc Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 16:20:10 -0400 Subject: [PATCH 65/68] Update corner_cases.two_tumor_seq_allele.out.uniprot.txt From 8e94f9c25f346186e2a7936fbf0669858d70f532 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 16:21:45 -0400 Subject: [PATCH 66/68] Update corner_cases.two_tumor_seq_allele.out.uniprot.txt --- test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt b/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt index 2f853bcf..31d37666 100644 --- a/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt +++ b/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt @@ -2,5 +2,5 @@ #isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A 8 17796382 17796383 AC AAC GT ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS -KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 12 49435045 49435045 G C - ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 8 17796381 17796383 AAC AAC AGT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C 12 49435045 49435045 G C - ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT 8 17796381 17796383 AAC AAC AGT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS From ebf8d4aa161c26e16cf6035bfb8af5b2adf5a655 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 16:24:55 -0400 Subject: [PATCH 67/68] Update config.yml --- .circleci/config.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index 1c643606..5094480b 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -53,6 +53,10 @@ jobs: name: "check if minimal example maf file still the same when annotating with uniprot transcripts" command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar -r --filename test/data/minimal_example.in.txt --output-filename test/data/minimal_example.out.uniprot.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/minimal_example.out.uniprot.txt || (echo simple MAF uniprot output changed test/data/minimal_example.out.uniprot.txt && exit 1)' + - run: + name: "check if columns prefixed by IGNORE_Genome_Nexus_Original are immutable" + command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar -r --filename test/data/immutable_columns_test.in.txt --output-filename test/data/immutable_columns_test.out.uniprot.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/immutable_columns_test.out.uniprot.txt || (echo simple MAF uniprot output changed test/data/immutable_columns_test.out.uniprot.txt && exit 1)' + - run: name: "check if corner cases example maf file still the same when annotating with uniprot transcripts" command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar -r --filename test/data/corner_cases.two_tumor_seq_allele.in.txt --output-filename test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt || (echo simple MAF uniprot output changed test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt && exit 1)' From 8f33a67af40091600b8c13e0c9ae387ad965c7f2 Mon Sep 17 00:00:00 2001 From: as1000 <32502256+as1000@users.noreply.github.com> Date: Wed, 24 Mar 2021 16:28:19 -0400 Subject: [PATCH 68/68] Added dbSNP_RS --- test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt b/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt index 31d37666..2f853bcf 100644 --- a/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt +++ b/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt @@ -2,5 +2,5 @@ #isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A 8 17796382 17796383 AC AAC GT ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS -KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C 12 49435045 49435045 G C - ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT 8 17796381 17796383 AAC AAC AGT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 12 49435045 49435045 G C - ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 8 17796381 17796383 AAC AAC AGT ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS