I have few novel mutations with IVS nomenclature and I want their respective genomic positions. For the same, I require the intronic positions of the variants to give as input in Mutalyzer to extract their genomic positions.
Can anyone suggest a tool or a way with which I can convert the IVS nomenclature to a numeric value i.e exact position of the nucleotide?
Thanks!!
Dear Khyati,
Correct me if I'm wrong. You have e.g.:
NM_000548.3:IVS39+1G>A
and want to convert it to
NC_000016.10:g.2087942G>A or NG_005895.1:g.43637G>A.
I always do it manually. With the IVS nomenclature you know your intron of interest. You can check its coordinates in a genome browser (e.g. UCSC, IGV) and calculate your variant for the genomic position. If you need gene nomenclature, you can check it in your NCBI Reference Sequence and do the same.
Hi Michele,
Yes you got me right!!
From your suggested method, suppose my variant is IVS20-68, how should i look the intron in UCSC?
You just have to add c. before IVS20-68 and give as input in Mutalyzer. You would get the respective genomic position