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zwdzwd / transvar

TransVar - multiway annotator for precision medicine
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Deviation from HGVS recommendations #48

Open ktrien opened 3 years ago

ktrien commented 3 years ago

Below a second issue concerning a called variant, which deviates from the HGVS guidelines. Using the current version (transvar v2.4.1) we use, the output of a specific variant is the following:

SRSF2 c.284_307del24 p.(Pro95_Arg102delProProAspSerHisHisSerArg)

However, following the HGVS guidelines, the 24 should not be reported, as this is excess information. (https://varnomen.hgvs.org/recommendations/DNA/variant/deletion/)

The same applies on protein level where the deleted amino acids should not be summed up: (https://varnomen.hgvs.org/recommendations/protein/variant/deletion/)

I compared the updates on github (our current version 2.4.1 with the last new updated version (v2.5.9)) but could not see any commit solving this issue.

Is there any adaptation on transvar possible in order to get the correct HGVS-recommended variant description?

Thanks in advance! Kind regards,