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Reading the Wikipedia page for SNPs I find the sentence "Almost all common SNPs have only two alleles." This is consistent with terminology elsewhere, such as the therm "Minor allele frequency", which references the least common allele, which implies there are generally only two alleles for a given SNP.

But there are 4 common nucleotides, A, T, C, and G. Why wouldn't it be common to have 3 or 4 alleles at a certain location? The only way this seems possible to me is if strand is ignored, and so at any given location "A" and "T" are considered the same allele and "C" and "G" are considered the same allele. Is this the case, or am I misunderstanding things.

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Well, though it is possible to have SNPs of more than two alleles, and some exist, due to the low probability of having a basepair change twice in the same base-pair (there are aproximately 3.000 Mb in the human genome) and have it in more than 1% of the population (remember we are talking about single nucleotide polymorphism) to classify as a polymorphism is a very rare phenomenon.

I can check the maths for it if you need it, but it's just matter of probability.

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  • $\begingroup$ To be sure I understand, the idea is that say 100% of a population has an "A" at some loci at some point in time. Then say a mutation causes a member, call her Alice, of the population to have the loci at that base replaced with a "C", and they pass that mutation on to their offspring. After some time, that loci would be considered a SNP if enough of Alice's descendants survived such that they make up 1% of the population. The only way for another allele to exist is is if someone else at some other point in time ALSO has a mutation at that loci that switches away from "A" or "C", which is rare $\endgroup$
    – Paul
    Commented Aug 20, 2015 at 21:38
  • $\begingroup$ The percentage varies between definitions of polymorphisms, some say 1%, some say 5%, but you got the idea. You have to think that is not a loci, but rather a single position of a loci. Even if all locis accumulated 1 single base mutation each generation with a 2.5 kb length (that is the average loci if i remember correctly) it would still be 1/2500 probability of affecting the aame letter and times 2/3 (as one of the mutations would be a reversion to the original). So yeah, it is highly improbable. $\endgroup$
    – Athe
    Commented Aug 20, 2015 at 22:17

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