Could someone help me check what genomic position is this variant nomenclature referring to ?
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3.2 years ago
curious ▴ 780

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

  1. Does it seem right?
  2. IIs there a better way to do this?
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Does this maybe appear in the NCBI ClinVar database?

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UGT1A9 766G>A (D256N)

This is not the full name in HGVS format. If you have that you can use a tool like Mutalyzer.

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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?

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Based on UGT1A9 being the gene name, if nucleotide change corresponds to the correct AA change then you seem to have the right answer.

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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 NC_000002.12:g.233672700G>A or NG_002601.2:g.87957G>A or chr2:g.233672700G>A or 2:g.233672700G>A.

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.

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