If you’re using VarSome or VarSome Clinical, you may have noticed the “Submit to ClinVar” button. However, if you are unsure what steps are required before a submission can be completed, this article will help you get started. For a more detailed explanation, please visit our Help Center.

Please note that this feature is not yet supported for CNVs.

Submitting to ClinVar from VarSome

Step 1: Register and Get API Access

• Register your details at the ClinVar Submission Portal.
• Request a Service Account and API key from ClinVar by emailing clinvar@ncbi.nlm.nih.gov. 

Note: These steps are mandatory to enable submission via VarSome and VarSome Clinical. 

Step 2: Select the Variant 

• Log in to VarSome.
• Find your variant of interest.
• Click ‘Submit to ClinVar’ in the ClinVar Card on the variant page.
  

Note: If your API Key has not yet been configured, you will be prompted to set it up.

Step 3: Complete Submission Form

You will be asked to fill in several fields:

• Describe how you classified the variant and the supporting evidence.
• Evidence may be a citation, URL, or file name. 

• Add citation(s) - Database identifier (e.g., PubMed ID) or URL, not both. 
• Select a clinical significance label
• Optional: add explanation, assertion score, and last evaluation date (yyyy-mm-dd format). 
• If ‘Drug Response’ or ‘Other’ is selected, please add relevant explanations. 

Note: If you provide a PubMed ID as a citation, the system will validate the citation and display the abstract. 

• Provide the condition name or ID related to the drug response.

• Specify the condition name or ID.
• Optional: Include local ID or local key. 

• Indicate whether affected individuals were observed. 
• Provide allele origin and, optionally, clinical features. 

• Add features by name or database ID. 
• Describe how the features were collected. 
• You can add a free-text comment with further clinical or diagnostic context. 

• Submission name (or use default submission ID).
• Record status (new/update).
• Release status (public/hold).

• Describe the variant using HGVS or chromosomal coordinates (not both). 

Once you have completed the form, click Submit. You can then track the submission status in your VarSome profile. 

Status options include: 

• Submitted
• Processing
• Error
• Processed (not published)
• Published

Submitting from VarSome Clinical 

Step 1: Select Analysis

From the Dashboard or Analysis page, select the analysis of interest. 

Step 2: Choose Variant

In the results table, click the ‘Germline Classification’ card on the Results Analysis page. In this card, you’ll see the ‘Submit to ClinVar’ button, allowing you to complete your submission in the same way described above. 

Step 3: Submit

Once submitted, you can track the status of your submission as described above. 

Additional Support

For more support with VarSome or VarSome Clinical, contact our support team: support@varsome.com. 

For help with ClinVar API/accounts, please contact: clinvar@ncbi.nlm.nih.gov.