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Factor V Leiden Mutation missing because of Transcript liftover #412

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einicke opened this issue Mar 25, 2024 · 0 comments
Open

Factor V Leiden Mutation missing because of Transcript liftover #412

einicke opened this issue Mar 25, 2024 · 0 comments
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@einicke
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einicke commented Mar 25, 2024

Describe the bug
Factor 5 Leiden Mutation c.1601G>A p.Arg534Gln is the reference in hg37:chr1:169,519,049-T-T, this was fixed in hg38:chr1:169549811-C-T.

The Mane Transcript of F5 NM_000130.5 (and also the older NM_000130.4) were uptated earlier and have the correct G as a reference.

In Varfish, the heterozygous variant is first annotated as hg37:chr1:169,519,049-T-C and then predicted as NM_000130.4:c.1601G>G in the result table. The ClinVar linkout also leads to the benign NM_000130.5(F5):c.1601= (p.Arg534=).

Homozygous mutations will be therefore missed at all and heterozygous variants will be classified as benign.

Expected behavior
Variant should be called correctly as c.1601G>A p.Arg534Gln

@einicke einicke added the bug Something isn't working label Mar 25, 2024
@xiamaz xiamaz moved this to In review in Release Planning Mar 27, 2024
@xiamaz xiamaz self-assigned this Mar 28, 2024
@xiamaz xiamaz moved this from In review to Ready in Release Planning Mar 29, 2024
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