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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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Update genecode mapper #269

Open cheanney opened 1 month ago

cheanney commented 1 month ago

Hi,

We are attempting to annotate all variants for the KRT86 gene. Based on the HG38 genomic location of KRT86, we obtained all gnomAD v4 variants within this region. While exploring the OpenCRAVAT results, we discovered that all variants were assigned to AC021066.1 instead of KRT86. The Ensembl transcript ID is ENST00000293525.5. We verified this transcript on Ensembl, and it is indeed assigned to KRT86. We then checked the Gencode version used in the mapper, which is version 33. The latest version is 44. We are wondering if the Gencode mapper in OpenCRAVAT can be updated.

Here is one of the variants we investigated:

chr12 52306237 G A Yes AC021066.1 ENST00000293525.5

Thanks

RachelKarchin commented 6 days ago

Sorry for our slow response. This is a hugely important issue and we will be prioritizing it. Stay tuned for updates.