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broadinstitute / gnomad-browser

Explore gnomAD datasets on the web
https://gnomad.broadinstitute.org
MIT License
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Differentiate ClinVar variants with conflicting interpretations of pathogenicity #751

Open nawatts opened 3 years ago

nawatts commented 3 years ago

Currently, ClinVar variants with multiple interpretations are all labeled as "Conflicting interpretations of pathogenicity". On the variant page, details about each submission can be seen. On the gene/region/transcript pages, however, there's no way to get more detail about the conflict.

The ClinVar track on these pages should include whether the variant is "Conflicting (P/LP vs. VUS/LB/B)” or “Conflicting (VUS vs. LB/B)".

nawatts commented 3 years ago

https://atgu.slack.com/archives/CNLMF0JLV/p1617201073047100

Shicheng-Guo commented 3 years ago

Hi Nick,

I download VCF files and try to find "likely pathogenic, Conflicting interpretations of pathogenicity" information, however, it looks ClinVar annotation is not existed in download VCF, right?

Thanks.

Shicheng

nawatts commented 3 years ago

ClinVar annotation is not existed in download VCF, right?

Correct. The ClinVar data displayed in the browser is downloaded from ClinVar about once a month. It is not included in the gnomAD release files.

https://www.ncbi.nlm.nih.gov/clinvar/docs/maintenance_use/#download https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_00-latest.xml.gz