The Variant Prioritization (VP) is a VCI feature requested by ClinGen Expert Panels curating variants to enable the discovery of prioritized variants for curation through filtering on select variant evidence data. Ultimately we plan for the VP to also support the sorting, updating and batch transfer of prioritized variants for curation at a larger scale within the VCI.

The VP supports the following filters: ClinVar Aggregated Clinical Significance, ClinVar Review Status, Molecular Consequences (limited to MANE select transcripts), gnomAD v.2.1.1 (subpopulations, total, male and female, and population filters for both exome and genomes), REVEL scores, and VCI interpretation status.

Filters can be added using the "+ add filter" button. Filter options are expanded using the right-handed arrow. Applied filters are displayed in the filter view.

Searches on the VP are currently based on the HGNC gene name. A list of all supported genes is displayed under the search bar on the search page. The VP will return all variants for the given gene identified to ClinGen’s Allele Registry, along with their associated data. This search process may take a few minutes.

Any user with an active curation interface login can access the VP. The VP can be accessed from the ClinGen VCI production interface. Select VP features for saving searches are restricted to users logged in as an affiliation.

To access the VP from within the interface, click on the “Variant Prioritization” button in the blue navigation bar.

The filter view has the following sections:

a Displays the search term(s) used

b Displays the filters applied

c Toggle the "Columns" section to control the data displayed in the "Selection" section

d Use the "Add Filter" button to add new filter(s)

e The Filter Progress Bar shows how many variants were initially selected for, how many match and don't match the applied filters, and how many variants are actively selected in the selection section.

f The Selection section displays the data for filtered upon variants and enables specific variant selection.

Once variants of interest have been identified, a user can select them using the checkbox on the left side of the main table.

Users can then use the orange 'Transfer' button to download the selected variants and associated data into a .csv output.

The data in the VP originates from multiple sources, specifically: Ensembl, MANE, gnomAD, myvariant.info, ClinVar and the VCI itself.

ClinGen-built tools such as the ClinGen Allele Registry, the Linked Data Hub, the Data Ingest Service and the ClinGen Data Streaming Service, along with a streaming microservice pull and collate the data for users in the VP to search, filter, and prioritize variants on.

The VP "Columns" view allows a user to customize the table output they see. Users can drag and drop reorder the column display, add or remove columns, and fine tune which data is displayed.