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Question regarding HGVS nomenclature for 2 variants separated by 2 normal nucleotides #40

Open harryiland opened 2 weeks ago

harryiland commented 2 weeks ago

Two TET2 variants in cis were obtained: NM_001127208.2:c.1484_1486del and NM_001127208.2:c.1489del

According to HGVS recommendations, these should be described as: NM_001127208.2:c.[1484_1486del;1489del] and the protein changes should be described as p.[Thr495del;Thr497Leufs*36]

However Mutalyzer converts this to NM_001127208.2:c.1484_1489delinsTG p.Thr495Metfs*37

Is this a failure of Mutalyzer or is the delins nomenclature acceptable?

Thanks

mihailefter commented 2 weeks ago

There is an HGVS community consultation taking place regarding the description of variants that are close to each other. Currently, Mutalyzer normalizes the two DNA variants as a single delins, with the protein description being predicted accordingly. However, we are working on a new implementation that provides a normalized description that keeps the two DNA variants separate. At the moment, we are unable to predict a protein description for this, but we are working on improving this as well (p.([Thr495del;Thr497Leufs*36]) seems like a valid prediction).