VP Help

Variant Prioritization Feature Help Documentation

Table of Contents

1. Introduction
2. Access
3. VP Searches
4. The Filter View
5. Filters
6. Columns
7. The VP Data Pipeline
8. Data Output
9. Saving Searches
10. Loading Searches

1. Introduction

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 that the VP will also support the sorting, updating and batch transfer of prioritized variants for curation at a larger scale within the VCI.

2. Access

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

To access the VP from within the interfaces, click on the “Variant Prioritization” button in the top right of the screen.

3. VP Searches

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.

4. The Filter View

The filter view has the following sections: a. The search term used for the search b. 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 filters 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.

5. Filters

6. Columns

7. The VP Data Pipeline

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.

8. Data Output

9. Saving Searches

10. Loading Searches