What Is The Meaning Of Maf Terms In Snp?

Question

[Frewise]

Could somebody please help me understand:what is the meaning of marked region, sometimes which appears to be "G=" and sometimes appears to be "T=", so what does T or G stand for? These two pictures are generated from link text and link text Thanks for your time!

[Pierre Lindenbaum]

huuuu??? did you just click on the link http://www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html#gmaf?

Answer 1

[Jorge Amigo]

a SNP is defined as a variable single base position in the genome, which should appear with a frequency of at least 1% in a particular population in order to consider it as polymorphic. although this definition is still valid, the term variant is being slowly favoured, because the capabilities we have now to detect rare variants allow us to have recorded in dbSNP events that could have occurred on a single genome. but the population genetics under such definitions always imply thinking about frequencies, in order to be able to discriminate when selecting SNPs for a study, or to understand the effects of a variant found on a NGS study, for example.

as mentioned by Rubal, MAF states for Minor Allele Frequency, but it is always critical to know not only which population or samples is referring to, but also which allele is referring to. this last part goes for non bi-allelic variants, whose MAF is usually reporting the frequency of the second allele, and not the minor one. we tend to think that all SNPs are bi-allelic, and most of them they are, but it's always a good idea to check which allele the MAF is exactly reporting.

summarizing Pierre's comments too on this answer, if you just follow the link on that blue underlined MAF/MinorAlleleCount label you would see the detailed documentation about this, which tells you that the MAF is always referred to the whole sample set available which described the variant, independently of the populations where they came from. this is very important too, as when doing SNP selection for a study (for instance) you may want to select a SNP with low MAF on a particular population (say a particular MAF of 0.1), but that may be of homogenously distributed through the entire world (say a global MAF of 0.4), or of course viceversa (a global MAF of 0.1 but evenly distributed on the population you are looking at). you would then need to carefully study that particular SNP in the population/s of interest in order to make sure that you aren't leaving anything behind.

Answer 2

[Rubal]

Isn't this the minor allele frequence of the G and T snp in a specified population? With T or G being the nucleotides.

[Bert Overduin]

The confusing thing here is that dbSNP for instance for rs1129332 reports the alleles (A/G) relative to the reverse strand of the genome, while the minor allele (T) is reported relative to the forward strand. Messy to say the least .... Ensembl at least reports everything relative to the forward strand (http://www.ensembl.org/Homo_sapiens/Variation/Population?r=1:2335710-2336710;v=rs1129332;vdb=variation;vf=8393181).