ClinVar is a freely available submission-driven database for information about genomic variation and its relationship to human health. ClinVar holds more than 1.5 million variants, and is powered by submitters around the world, who provide us with their assessments, the evidence, and the criteria they use to guide their interpretation process and come to their conclusions. To streamline the ClinVar submission process, we are simplifying how submitters provide their assertion criteria. In the past, assertion criteria were provided for each variant. Moving forward, one single set of assertion criteria will be associated with an entire submission regardless of the number of variants.
What that means for the submitter
Submitters using the submission spreadsheet templates should plan to switch to the new versions on November 21, 2022. These submitters should also plan to group variants within a single file submission by assertion criteria. A submission will reference one set of assertion criteria only, and these criteria must apply to every variant classification in the submission.
As part of this change, the submission spreadsheet templates have been updated to remove the columns for data related to assertion criteria and an error message will be provided if older versions of the spreadsheet template are used going forward.
Providing new files for assertion criteria:
- Preparing your submission: A submission can reference one set of assertion criteria only, and these criteria must apply to every variant classification in the submission. Organize your submission files by assertion criteria.
- Assertion criteria files will now only be uploaded from the organization’s landing page in the ClinVar Submission Portal. This applies to all submission pathways (file, wizard, or API).
- Upload the new files for assertion criteria on your landing page in the ClinVar Submission Portal, independent of a submission.
- Assertion criteria is a document that includes both the terms an organization uses to classify a variant (e.g. uncertain significance, benign, or pathogenic) AND the criteria used to assign a variant to any of these classifications.
- For wizard or file submissions, choose the assertion criteria on the submission’s Assertion criteria tab in the ClinVar Submission Portal. Note that Citation IDs (PubMed ID, PubMed Central ID, or DOI) will be selected directly from the Assertion method tab as well.
- Previously reported assertion methods will still be available for use in new submissions.
What’s new?
The new spreadsheet templates (versions L1.7 and 4.3) no longer include the following columns:
- Assertion method
- Assertion method citation
As of November 21, 2022, you will need to switch to the new versions of the submission spreadsheet templates. We will no longer support previous versions.
New steps in submission
1) Adding Assertion Criteria – Organization Page
2) Uploading a new file for assertion criteria
3) Associating assertion criteria to a submission
Questions?
If you have questions or would like to provide us feedback, please contact us at clinvar@ncbi.nlm.nih.gov.