GN Immutable (chr,start,end,ref,alt1,alt2)

.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)'

annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java

@@ -231,6 +231,20 @@ public AnnotatedRecord convertResponseToAnnotatedRecord(VariantAnnotation gnResp
             // variant attributes (pos,ref,alt1,alt2) to be mutable?
         }
 
+        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),
                 annotationUtil.resolveEntrezGeneId(canonicalTranscript, mRecord, replace),
@@ -270,6 +284,12 @@ public AnnotatedRecord convertResponseToAnnotatedRecord(VariantAnnotation gnResp
                 mRecord.getT_ALT_COUNT(),
                 mRecord.getN_REF_COUNT(),
                 mRecord.getN_ALT_COUNT(),
+                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),

annotator/src/main/java/org/cbioportal/models/AnnotatedRecord.java

@@ -105,6 +105,12 @@ public AnnotatedRecord(String hugoSymbol,
         String tAltCount,
         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,
         String hgvsc,
         String hgvsp,
         String hgvspShort,
@@ -157,6 +163,12 @@ public AnnotatedRecord(String hugoSymbol,
             tAltCount,
             nRefCount,
             nAltCount,
+            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;
@@ -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.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");

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 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<String, String> additionalProperties = new LinkedHashMap<>();
     protected List<String> 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<String, String> 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<String, String> 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.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();
     }
@@ -441,6 +455,54 @@ public void setN_ALT_COUNT(String nAltCount) {
         this.nAltCount = nAltCount;
     }
 
+    public String getIGNORE_GENOME_NEXUS_ORIGINAL_CHROMOSOME() {
+        return this.IGNORE_Genome_Nexus_Original_Chromosome == null ? "" : this.IGNORE_Genome_Nexus_Original_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 getIGNORE_GENOME_NEXUS_ORIGINAL_START_POSITION() {
+        return this.IGNORE_Genome_Nexus_Original_Start_Position == null ? "" : this.IGNORE_Genome_Nexus_Original_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 getIGNORE_GENOME_NEXUS_ORIGINAL_END_POSITION() {
+        return this.IGNORE_Genome_Nexus_Original_End_Position == null ? "" : this.IGNORE_Genome_Nexus_Original_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 getIGNORE_GENOME_NEXUS_ORIGINAL_REFERENCE_ALLELE() {
+        return this.IGNORE_Genome_Nexus_Original_Reference_Allele == null ? "" : this.IGNORE_Genome_Nexus_Original_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 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 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 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 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) {
         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("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");
     }
 }

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	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

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	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