Genomic coordinates from traditional HGVS variants

Question

[hannes]

Does anyone know of a reliable workflow to convert traditional/deprecated HGVS variants such as "HBB:IVS2+705T>G" to genomic coordinates or current Sequence Variant Nomenclature (http://varnomen.hgvs.org)?

I'm aware of the hgvs and pyhvgs Python packages, but those don't understand the deprecated notation.

Many thanks!

[cpad0112]

Try ensembl variation api

[finswimmer]

I'm not aware of a tool for the depecrated notations. Whatever tool you use you have to be aware that the result could be ambiguous as the hgvs notation depends on the transcripts and of course one gen can have multiple ones.

[hannes]

@finswimmer Thank you, maybe I should've been more explicit.

The HGVS Recommendations (https://www.hgvs.org/mutnomen/disc.html#tradition) say this about traditional descriptions:

Although annoying, traditional descriptions should not be used anymore. When one uses the recommended descriptions it will be only a matter of time until also the experts get acquainted. The recommendation is to list in the variant summary Table official and traditional names next to each other in separate columns, like c.88+2T>G and IVS#+2T>G, p.Phe508del and delF508, or c.24dupG and Cd8/9+G.

The problem is that there are still a lot of resources out there that use this notation, e.g. DBASS (http://www.dbass.org.uk), but also more recent papers: https://rdcu.be/7nT9.

Of course what's even worse is that some of these resources don't specify the transcript ID they're referring to, but only the gene name. The best way to deal with this is probably just to use the canonical RefSeq transcript.

[finswimmer]

Hello hannes,

I know these recommendation and I fully support the opinion not to use things like IVS+. Without knowing the transcript it is much harder to find the genomic the position.

I fear one have to write a program that first find all possible positions for the given transcripts of a gene, filter out those where the reference bases doesn't much. If you have luck there will be only one result left.

(Nice excercise. Maybe I have some time next week to do something with python ...)

fin swimmer

Answer 1

[Emily]

You could try the Ensembl VEP, which allows you to input a list of variants and gives you loads of information about them, including known rsIDs and genomic loci. HGVS is a valid VEP input.

[hannes]

Unfortunately, VEP also doesn't seem to understand the deprecated nomenclature that uses IVS# for intronic variants.