Albeit built for mapping protein sequence intervals, my script "protein2genome.pl" can do this. It ships with the variant annotation tool CooVar.
Here is how it works. First you need a GFF or a GTF file with the coordinates of your genes. To test your specific example, I created a GTF file that contains only the first isoform of the BRAF gene, but you could also work with GFF/GTF files containing all human genes and isoforms or containing genes from any other organism. Then you can run protein2genome.pl like this:
echo "ENST00000288602 . . 600 600 . . . ID=V600E" | perl protein2genome.pl BRAF-001.gtf
Produces the output:
7 . . 140453135 140453137 . - . ID=V600E(ENST00000288602);segment=1of1;p_start=600;p_end=600
Explanation: I am basically piping a GFF-compliant input line specifying the ID of the transcript and the position of the protein sequence change into the script. The script then outputs the mapped genomic coordinates (chromosome 7, codon start=140453135, codon-end=140453137).
A more detailed explanation of input and output formats can be found here.
I would say this script is more useful for non-model organisms, because for model organisms with associated databases you have other possibilities to do that (see other answers in this thread, for example the Ensembl REST API which is quite neat).
Here is an example of what I was talking about: BRAF.p.V600E:c.1799T>A
Given just this information, is there a way I can get to the genomic coordinates. I guess there is the CDS position, can this direct us to the genomic location?
Here is an example of what I was talking about: BRAF.p.V600E:c.1799T>A Given just this information, is there a way I can get to the genomic coordinates. I guess there is the CDS position, does this help?