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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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Ambiguous annotation results #223

Closed cheanney closed 6 months ago

cheanney commented 6 months ago

First, I would like to say thank you for this wonderful too. This tool has significantly improved our workflow.

However, we've encountered some issues with ambiguous annotation results. Specifically, we're analyzing the following genetic variant: chr7 149528263 + G A This variant is based on the HG19 reference.

Using the openCravet platform, this variant is identified as intergenic. Yet, it's associated with COSMIC annotations as follows: COSMIC_ID: COSV65128555 COSMIC_TISSUES: [["NS", 1], ["large intestine", 1]] COSMIC_VARIANT_COUNT: 2 COSMIC_TRANSCRIPT: ENST00000378016.4 COSMIC_PROTEIN_CHANGE: R5063Q COSMIC_MATCH: Exact Match

We're seeking clarity on these conflicting annotations.

Thanks,

Anney

Screenshot 2024-03-20 at 2 05 37 PM
kmoad commented 6 months ago

This variant maps to a transcribed pseudogene, SSPOP/SSPO. The exact variant has annotation in COSMIC https://cancer.sanger.ac.uk/cosmic/mutation/overview?id=116634497. We don't map pseudogene variants even when they are transcribed, we instead report them as intergenic.

We do offer a pseudogene annotator, which annotates this variant with the same transcript as COSMIC.