I have genomic mutation and corresponding protein mutation for several genes, for example c.2503G>T (genomic) and p.D835Y (protein) for FLT3 gene. What is the easiest way to determine the genomic location for this variation?
Before you start, you need to get the transcript ID first for your gene (in your case, FLT3). Suppose we use the isoform 1 of FLT3, the transcript ID will be ENST00000241453. Then just paste the bellowing to the browser
So you genomic location will be chr13:28018505.
I made a VCF line with this information
chr13 28018505 . C A . PASS DP=8194;AF=0.074;NP=4;PV=0.0
Then I run the annovar, the output is FLT3:NM_004119:exon20:c.G2503T:p.D835Y. So should work, just need to pay attention the genomic coordinate is GRCh38 rather than hg19