Hi.

I am wondering a term with SIFT score.

I think that SIFT refers to some measurement of SNPs, and while reading Annovar paper, I saw below sentence as follows:

> Finally, Annovar can filter specific variants such as SNPs with >1% frequency in the 1000 Genomes Projects, or non-synonymous SNPs with SIFT scores > 0.05.

Regarding above sentence, I ask you two questions.

1. I think that 1% frequency is a little bit low allele frequency. Dose it have an effect to filtering irrelevant snp variants? I don't think so..
2. SIFT-score threshold is about 0.05 as shown in above sentence. What does SIFT means about and threshold of 0.05 might be effect on filtering variants?
<p>To answer your first question, 1% is the standard cutoff used to describe the difference between &quot;common&quot; and &quot;rare&quot; variants. Depending on your study, you might want to change that. For example, in a GWAS for a common trait, you might be interested only in variants that are above a certain frequency in the population, whereas if you&#39;re looking at rare Mendelian traits you might only want very low frequency variants. You may also want to narrow this down to a specific population, eg for a GWAS in African Americans, you would be interested in variants common in African populations. Steve mentioned the VEP, which allows you to filter variants by frequency, choosing your own frequency, &gt; or &lt; and pick a population of interest.</p>
