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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 to the variant title logic #165

Closed cgpreston closed 1 year ago

cgpreston commented 2 years ago

Please update the variant title logic as follows: 1

  1. Use the "communitystandardtitle" from the allele registry if it exists
  2. If not 1, use the ClinVar variant title
  3. If neither 1 or 2 exist, use the genomic coordinates

SP ticket: https://broadinstitute.atlassian.net/browse/CGSP-462

Also please update the hoverover next to the variant title. Current text:

Screen Shot 2022-07-13 at 1 36 51 PM

Desired text: The HGVS is based on the Community Standard Title provided by the ClinGen Allele Registry, if there is no Community Standard Title, then the ClinVar Preferred Title is used. If there is no ClinVar Preferred Title, then the HGVS is based on the GRCh38 genomic coordinates.

cgpreston commented 2 years ago

Please note that (per personal communication with Kevin) the CAR won't update to the latest version of MANE until late April 2022, and this ticket should be implemented after that update occurs. - this has been updated

cgpreston commented 2 years ago

Please note, the MANE select transcripts are not currently being marked in the VCI, please fix that as well as part of this work.

cgpreston commented 2 years ago

If possible please also implement https://github.com/ClinGen/gene-and-variant-curation-tools/issues/38, which are indicated in the Allele Registry now.