Silent mutations about mutalyzer2

[jfjlaros]

At the time that Mutalyzer was written, the goal of the HGVS nomenclature was to describe variants, over time this has shifted towards describing non-variants as well. This conflicts with the primary goal of the HGVS nomenclature, namely the disambiguation of variant descriptions.

Our position is that it should be possible to get a protein description from the original protein sequence and the observed protein sequence, independent from the underlying nucleotide changes. This is the only way to get the same description for variants that have the same effect, which is, in our opinion, a useful and desirable property of a variant description language.

In the Mutalyzer project, we have chosen to make variant disambiguation the priority, which means that the HGVS rules that conflict with this, can not be implemented.

Unfortunately, we have not been able to convince the HGVS nomenclature committee that this is a problem.