1
$\begingroup$

Wikipedia citing Nature defines SNP to be a one where each (thus the lowest frequency) allele exceeds some percentage threshold in the population. But I see a lot of papers and books calling such an entity a "common SNP" rather than leaving it unqualified example 1, example 2. Are they using a different/simpler definition of SNP?

Another book says that "SNPs most commonly refer to single-base differences in DNA among individuals" with no qualification on frequency. So I'm guessing those two sources that define "common SNP" use this broader definition of SNP. Would anyone venture a guess which definition of SNP is more prevalent? There's no discussion on the topic of the definition itself on the talk page of the Wikipedia SNP article...

$\endgroup$
1
$\begingroup$

I think the convention is that a point mutation with a frequency of 1% or more of the population is a 'Single Nucleotide Polymorphism' and anything lower would be 'Single Nucleotide VARIATION'. So regardless of the frequency, any point mutation would be a 'Single Nucleotide Variation'. At higher (more significant) frequencies, we call it a 'Single Nucleotide Polymorphism'. Some may choose to name an SNP of high frequency (for example with a frequency of 15% or more of the population) as a 'common SNP'. In reading, texts will usually give you the percentage for the SNP and their naming choice should make sense. There is no fixed systematic number at which an SNP becomes 'common' or 'rare', since anything less than 1% won't count as one.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.