How to tell which exon does a variant located?

Question

[maricom]

Hi,

I have a variant data like this. ABL1 NP_005148.2:p.Thr315Ile NM_005157.5:c.944C>T

How can I find which exon (exon 1,2,3,,,,etc.) is this variant located?

Thank you!

[swbarnes2]

Note that there is no single exon number for a given position, as different transcripts will have different numbers of exons. You'd have to say, "this is in exon three of this transcript ID"

[Ram]

OP gives a specific NP/NM ID, so the exon number concept is valid here. IMO if they'd even included g. or chr co-ordinates, this note would make sense.

Answer 1

[Ram]

Run the variants through VEP, that should give you exon number. I ran your HGVS NM_005157.5:c.944C>T through VEP and got this: https://useast.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=PzhcF4QeFmCbznFz-9089901