Someone asked me for what genomic change (position:ref>alt) this variant is referring to, embarrassingly I am having a hard time:
What I was given Given:
UGT1A9 766G>A (D256N)
I think 766G>A is referring to a CDS change (from coding sequence), or the the portion of a gene's DNA or RNA that codes for protein.
Working backwards from CCDS if I change the 766th nucleotide under "Nucleotide Sequence" (which is a G) to and A, this results in a protein sequence change D256N, so I then BLAT the 766 nucleotide string to find this G sits on the + strand at 2:233672700.
So I think the change in chrom:pos:ref>alt on build 38 , where ref allele refers to the reference allele on the forward strand is 2:233672700:G>A or rs58597806
- Does it seem right?
- IIs there a better way to do this?
Does this maybe appear in the NCBI ClinVar database?
This is not the full name in HGVS format. If you have that you can use a tool like Mutalyzer.
So in future if I have HGVS format, I understand I can use the tool. Regardless would my sleuthing here have given me the correct answer or is it still ambiguous?
UGT1A9being the gene name, if nucleotide change corresponds to the correct AA change then you seem to have the right answer.
1. Does it seem right?
Manual back referencing is correct. But it's a multi-transcript gene. cSyntax in OP is ambiguous and it should be (for this protein)
NM_021027.3:c.766G>A. gSyntax is incorrect and you need to note down the genome build somewhere. correct gSyntax is
2. Is there a better way to do this?
A variant HGVS representation must be unambiguous, as much as possible. Visit HGVS site for reference.