Mutalyzer 2: next generation HGVS nomenclature checker

Motivation: Unambiguous variant descriptions are of utmost importance in clinical genetic diagnostics, scientific literature and genetic databases. The Human Genome Variation Society (HGVS) publishes a comprehensive set of guidelines on how variants should be correctly and unambiguously described. We present the implementation of the Mutalyzer 2 tool suite, designed to automatically apply the HGVS guidelines so users do not have to deal with the HGVS intricacies explicitly to check and correct their variant descriptions. Results: Mutalyzer is profusely used by the community, having processed over 133 million descriptions since its launch. Over a five year period, Mutalyzer reported a correct input in similar to 50% of cases. In 41% of the cases either a syntactic or semantic error was identified and for similar to 7% of cases, Mutalyzer was able to automatically correct the description.

Automated summary

The Human Genome Variation Society provides guidelines on accurately describing genetic variants, with the Mutalyzer tool suite being able to automatically apply these guidelines for users to check and correct their descriptions. Mutalyzer has successfully processed over 133 million descriptions, with around 50% being reported as correct and able to automatically correct descriptions for approximately 7% of cases.