ClinGen / gene-and-variant-curation-tools

ClinGen's gene and variant curation interfaces (GCI & VCI). Developed by Stanford ClinGen team.
https://curation.clinicalgenome.org/
MIT License
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update gnomAD link to variant local region #344

Open cgpreston opened 8 months ago

cgpreston commented 8 months ago

Sub-ticket for gnomAD v4 update https://github.com/ClinGen/gene-and-variant-curation-tools/issues/47

The gnomAD link out in the VCI is now pointing to the genomic coordinates of the variant in gnomAD v2 4.0.0, of important note: v2.1.1 was on GRCh37, v4 is on GRCh38, which means the genomic mapping is incorrect. The users experience the following behavior: 1. For variants present in v2, the gnomAD link now gives an error message saying "variant not found" (ex: variant 21065) 2. For variants NOT present in v2, the gnomAD link to look +/- 30 bp will often map incorrectly (ex: variant 65692).

Please fix the link such that it goes to the correct coordinates for gnomAD v4 (on GRCh38), and update the text as shown:

Screen Shot 2023-11-07 at 11 56 40 AM

Requirements:

  1. The link should land on the gnomAD v4 variant page for variants present in gnomAD v4
    • The VCI language for these should be "see data in gnomAD v4.0.0"
  2. The link must be reconstructed to support +/- 30 bp of the variant on GRCh38 for variants not found in gnomAD v4
    • The VCI language for these should be "View the coverage of this region (+/- 30 bp) in gnomAD v4.0.0"
cgpreston commented 8 months ago

Relates to #47, see slides:https://docs.google.com/presentation/d/1-rZf4ZpQ0SkuBkdZ6WZqfKCPaDF9rfDrf1IgQ1YCm0A/edit#slide=id.g297f132bc0d_0_0

cgpreston commented 6 months ago

@liammulh , the gnomAD v4 links are now available in the allele registry: https://reg.genome.network/redmine/projects/registry/genboree_registry/by_caid?caid=CA2387254395, and in their JSON output, as well as the GRCh38 coordinates. In January 2024 can we revisit this ticket to add the links to v4?

Screen Shot 2023-12-18 at 12 53 58 PM