Implement automated CIViC AID submissions to ClinVar

[ahwagner]

We discussed implementing CIViC AID submissions to ClinVar on the 3/19/26 CIViC call. In implementing this, we will want to:

• Create a CIViC Core Team organization, a top-level org comprised of participants from the CIViC grants
• Assign current CIViC ClinVar API key to this new organization
• Assign CIViC Core Team Approver status to Editors in this organization
• Have approver team review all accepted CIViC AIDs for approval
• Update prior work on the ClinVar submission workflow to use singular API keys per org
• (NOT NEEDED; see below) @ahwagner to inquire with Melissa whether existing submissions can be moved from germline to somatic and if yes, how to do so.
• Backfill the submission IDs from prior submissions for update
• Generate and evaluate a dry run submission packet using the updated workflow
• Submit all approved CIViC AIDs supported by ClinVar

Our target is to complete the above activities ahead of the April 23rd CIViC meeting.

[acoffman]

Backfill the submission IDs from prior submissions for update

Is likely contingent upon the answer to

whether existing submissions can be moved from germline to somatic

[susannasiebert]

In addition to the above todos the following decisions were made:

In general, any organization we grant permission can approve an assertion and, if we have a ClinVar submission api key for the organization, these approvals will result in an automated submission to ClinVar under their organization. This may potentially result in multiple ClinVar entries for the same assertion, which is ok, and desired. Each organization should have their own SOPs for approving assertions.

Organizations will be responsible for deciding their own criteria for users in their organization that should be allowed to make approvals. For the new CIViC org, only editors will be allowed to approve (this is an SOP, not a constraint enforced by the database/code/etc).

All accepted assertions will be reviewed by editors in the CIViC org and, if meeting our curation SOPs, will be approved under the CIViC org. These approvals will result in 1-star submissions to ClinVar.

[ahwagner]

Backfill the submission IDs from prior submissions for update

Is likely contingent upon the answer to

whether existing submissions can be moved from germline to somatic

I'm not sure if there are any such submissions that need to be moved. I dug into this and couldn't find any germline submissions among our non-VHL records. I think @kkrysiak may have been seeing a display issue (feature?) on the submission status page that reports these submissions as germline and somatic, but if you investigate the individual VCVs it is clear that the submissions are properly categorized. Unless we have a specific instance of misclassification we can point to, I won't be moving forward on a request to address and we should consider this a moot issue.

UPDATE: I reviewed all of our submissions and @kkrysiak confirmed; no misclassified records. We should advance with our original plan to find submission IDs and preserve links to the previously curated records.