Conventions For Multi Allelic Snps

Question

[Andrea_Bio]

Hello

I am aware that the vast majority of SNPs have 2 alleles but as more sequencing data is becoming available, more and more SNPs are being found to have 3 or 4 alleles.

I am aware of the SNP ambiguity codes and conventions for describing SNPs. For example

A/G - simple biallelic SNP A/S - triallelic SNP (S=[CG])

But a triallelic SNP can have 2 consequences if it is within an exon (I don't think it can have more due to degeneracy of genetic code) : synonymous and non synonymous

Lets say we have the codon AT? and the question mark is a SNP, specifically the triallelic one give above A/C/G SNP

This coould give
ATA (reference) = Met
ATG = Met
ATC = Ile

You would write the amino acid alleles as Met/Ile

The reference allele gives rise to Met. However you don't know whether both C and G variants give Ile or just one of them. I would probably assume both C and G variants give rise to Ile but actually only the C variant does

Is there a convention you use in this scenario so you know which SNPs give which amino acids or do you have to simply spell it out for multiallelic SNPs

thanks

[Dave Gerrard]

What genetic code is this? I don't recognise ATA as Met.

Answer 1

[Larry_Parnell]

Tough question. Our favorite triallelic SNP is in a regulatory region of gene expression and so is not so complicated. My inclinations are to check the nomenclature guidelines at HGVS and to spell it out so that there is no ambiguity.

[Andrea_Bio]

i was reading this question and thought 'that sounds familiar!' then i realised i wrote it over a month ago!