update ClinVar API

[marc-sturm]

Dear ClinVar API Submitter,

Thank you for using the ClinVar Submission API! We are making changes to the API submission schema to support classifications of somatic variants. The details of the proposed update and some sample JSON files (with fake data - do not use this data!) are available on GitHub: https://github.com/ncbi/clinvar/tree/master/submission_api_schema.

Here's a high-level summary of the changes:

• three new submission set objects will be introduced: "oncogenicitySubmission" and "clinicalImpactSubmission" for somatic variants and "germlineSubmission" for germline variants
  -two new objects for the Observation of a somatic variant will be introduced: "presenceOfSomaticVariantInNormalTissue" and "somaticVariantAlleleFraction"

We propose to retain the object clinvarSubmission for a period of time to give our API submitters time to update to the new schema. However, we strongly encourage you to transition to the new schema soon to use "germlineSubmission" for your Germline Classifications as we are updating our terminology throughout ClinVar from "clinical significance" and "interpretation" to "classification".

We plan to make an updated test endpoint available on April 11, and we plan to put the new schema in production on May 15. If you have any comments or suggestions for changes to the schema, please contact us at [email protected] as soon as possible before May 15 so that we have time to make updates, if necessary.

Thank you for sharing data through ClinVar!

ClinVar staff

[leonschuetz]

Processing of CompHet variants containing CNVs/SVs (sometimes) fails.

• reported to ClinVar
• confirmed by ClinVar
• waiting for fix