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Properly handle selenoproteins #224

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holtgrewe opened this issue Oct 21, 2023 · 1 comment · Fixed by #265
Closed

Properly handle selenoproteins #224

holtgrewe opened this issue Oct 21, 2023 · 1 comment · Fixed by #265
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enhancement New feature or request

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@holtgrewe
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holtgrewe commented Oct 21, 2023

Is your feature request related to a problem? Please describe.
Certain transcripts have more than one stop codon. This leads to issues when trying to predict the effect using hgvs-rs (the issue already is in the Python-based hgvs). In this case, a prediction could still be made by ignoring the first stop codon. Of course, a note needs to be added.

Describe the solution you'd like
Implement appropriate behaviour to ignore the first stop codon where appropriate.

Describe alternatives you've considered
N/A

Additional context
Mehari log messages look like:

2023-10-21T07:20:59.106574Z DEBUG No consequences for VcfVariant { chromosome: "3", position: 49395540, reference: "G", alternative: "" } on NM_000581.4 (hgvs_p=p.?) - adding gene_variant;most likely the transcript has multiple stop codons and the variant lies behind the first.

@holtgrewe
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holtgrewe commented Nov 10, 2023

@holtgrewe holtgrewe changed the title Allow for sensible predictions if variant is behind stop codon Properly handle selenoproteins Nov 18, 2023
@holtgrewe holtgrewe linked a pull request Nov 19, 2023 that will close this issue
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