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Gene name in result list and variant details can differ

Open stolpeo opened this issue 1 year ago • 1 comments

Describe the bug For example for the gene HGNC:25322 - result list displays C12orf29 (previous symbol) while the official name is RLIG1

https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:25322

stolpeo avatar Nov 25 '24 10:11 stolpeo

RCA

The annotation of the gene for the variant in the variant details comes from annonars. In the result list, it is joined via the postgres query coming from the RefseqToGeneSymbol/EnsemblToGeneSymbol table. These tables are not up-to-date.

https://github.com/varfish-org/varfish-server/blob/1f6608d767f45fd37312d738fd33061fef7fcf5a/backend/variants/queries.py#L291

Solution

  1. Either we wait for the next-generation annotation step with mehari.
  2. or we substitute the join of the table with a call to annonars.

stolpeo avatar Nov 25 '24 12:11 stolpeo