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mutalyzer / mutalyzer2

HGVS variant nomenclature checker
https://mutalyzer.nl
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position-converter TO name-checker ERROR #469

Closed chrstphdm closed 5 years ago

chrstphdm commented 5 years ago

Hello,

I'm using position-converter to obtain a "c." notation for my specific transcript (chr7:g.55228053A>T to obtainNM_005228.3:c.1498+22A>T) : https://mutalyzer.nl/position-converter?assembly_name_or_alias=GRCh37&description=chr7%3Ag.55228053A%3ET

But entering this notation (NM_005228.3:c.1498+22A>T) in name-checker throw an error (Intronic position given for a non-genomic reference sequence.) : https://mutalyzer.nl/name-checker?description=NM_005228.3%3Ac.1498%2B22A%3ET

Did I miss something ?

Thank you.

jfjlaros commented 5 years ago

This is indeed confusing.

A transcript reference sequence does not contain any intronic sequences, this is why when we ask Mutalyzer to do a full check of this variant description, it raises this error.

The only way to check variants in an intron is to use a genomic reference sequence, for example:

`NC_000007.13(NM_005228.3):c.1498+22A>T`