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