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varfish-org / varfish-server

VarFish: comprehensive DNA variant analysis for diagnostics and research
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Gene name in result list and variant details can differ #2128

Open stolpeo opened 3 days ago

stolpeo commented 3 days ago

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 commented 3 days ago

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.