How to tell which exon does a variant located?
1 answer
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
Log in to answer this question.
More posts like this
-
Checking a SNP as common SNP or not using UCSC genome browser
written by maricom •
-
How to read gene variants
written by maricom •
-
Criteria for variant call
written by maricom •
-
How can I convert this kind of mutation's position to chromosomal position?
written by Ya •
-
operon for rRNA genes
written by maricom •
-
Strand information for cancer variants from COSMIC
written by Gene_MMP8
-
Location of intronic SNPs from exons
written by BAGeno
-
How to analyze the variants in non-coding regions
written by darklings
-
Chip-seq data and Hi C data
written by tarek.mohamed
-
the location of TFBS in genome / binding affinities caused by SNP
written by tonja.r
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"
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.