Adding ClinVar Submissions

As of August 8, 2024, the GCI now supports adding evidence from ClinVar submissions as well as published papers. ClinVar submissions can be added by querying the VCV and SCV record for a specific ClinVar variant.

The Variation ClinVar record or 'VCV' is the accession in ClinVar of aggregated data from all submitted records for classifications of the same variant. The number after the period in a VCV is the version of that particular variant accession. For example, VCV001679524.3 refers to version 3 of VCV001679524.

Further down the ClinVar variant page, this VCV record will also list all submissions related to that variant from different laboratories and research groups, each with their own Submitted record in ClinVar, known as an SCV.

'SCV' is the accession number assigned to a submitted record in ClinVar, e.g. SCV003931173.1.

The number after the period in the SCV is the version of that particular submitter accession. For example, SCV003931173.1 refers to version 1 of SCV003931173. If you submit a query to ClinVar based on that SCV, e.g. SCV003931173.1, you are directed automatically to the VCV page that includes this submitted record. The SCV accession number and version are displayed in the Submissions section.

Below is an example of what a ClinVar entry would look like in the GCI compared to a published PMID:

Both evidence sources can be added from the GCI landing page. The “Add” button will open a selection screen for retrieving and adding evidence.

After clicking the "Add" button, a selection screen will open. Users can search by PMID or ClinVar VCV ID (including VCV version number). To add a particular submitter's ClinVar entry to the GCI, enter their full SCV including the version number (for example, SCV003931173.1, not just SCV003931173).

To add a ClinVar submission as evidence in the GCI:

1. Click the “Add” button in the evidence source column.

   1. A new selection screen opens.

2. Enter ClinVar VCV ID (including version) in top field.

   1. A link to the VCV record will immediately appear.

3. Enter the SCV ID (including version) in the bottom field

   1. You can use the VCV link provided to find the SCV ID of the submitter you want to cite, if you don’t already have it.

4. Click the “Retrieve Evidence Source” button

   1. A preview of the ClinVar entry will appear below.

5. Click the “Add Evidence Source” button to add the ClinVar entry to the GCI

Based on the SCV entered, the Submitter, Variant title, date last updated and version number will be retrieved. If these details are correct, add that SCV to the Gene-Disease Record by clicking the “Add Evidence Source” button. The SCV will now appear in the Curation Central view for that Gene-Disease Record. Additional ClinVar submissions can be added to the Gene-Disease Record in the same way.

The ClinVar submission is now viewable and scorable in the GCI. Comments from the ClinVar submission appear where paper citations and abstracts normally would. Evidence can now be added and scored as usual.