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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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HMAF data displayed for variants in GCI #4

Open wrightmw opened 2 years ago

wrightmw commented 2 years ago

https://broadinstitute.atlassian.net/browse/CSP-26

HMAF in Evidence Summary Table. In the "Genetic Evidence: Case Level (variants, segregation)" table in the Evidence Summary in the GCI, the curators would like to include a new column that shows the HMAF calculated in the VCI. This new column would be placed after the "Variant" column, and called something like "HMAF". This column would display two values: Source: (e.g. ESP, gnomAD, ExAC, 1KG) Allele Frequency: #.####

Dependency on gnomADv4

wrightmw commented 2 years ago

Curators would like to see the HMAF from ExAC/GnomAD displayed in the GCI when they enter a variant. Currently they can link through to this information in the VCI.

Discussion in Thurs GCI WG call suggested that curators would like to see the both the HMAF and ClinVar assertion data ported across from the VCI for a variant: screen shot 2018-05-03 at 3 14 16 pm

screen shot 2018-05-03 at 3 14 24 pm

It was suggested that the two panels of data from the VCI ("Subpopulation with Highest Minor Allele Frequency" and 'Overall ClinVar Interpretation') shown above, could be added to the "Edit Variant Information" section of the GCI.