andrea_bio's question has got me thinking about SNPs in a bit more detail, and I find myself confused. I'm hoping someone can help clarify some of the nomenclature being used around SNPs/alleles - I'm finding it difficult to track down exact definitions.
In relation to SNPs, if there is a base that is known to take three different values, one of which is the reference value appearing in the reference genome (e.g. A in reference, T and G are known variants), do we:
(a) have 2 different SNPs (e.g. A->T, A->G)
(b) have just one SNP, which happens to have 3 different alleles? (e.g. A, T, G)
Also, NCBI's SNP primer page says that "On average, SNPs occur in the human population more than 1 percent of the time." Could somebody possibly clarify what is meant by this in more exact language? e.g. does it imply that the term SNP is only applied to variants if they are more common than 1% of the population?
Thanks for your time.