Question: Variant prevalence not listed
0
gravatar for chloe.p.oconnell
5.1 years ago by
United States
chloe.p.oconnell80 wrote:

Hi, 

I'm completing a variant analysis of rare variants found in the genomes of my cases vs. controls. I'm only looking at rare variants (variants where the alternate allele is present in less than 1% of the population, as determined by the 1000 genomes project alternate allele frequency). However, some of my variants (including many that have rsID #s) don't have an estimated 1000 genomes project allele frequency in dbSNP. For example, rs61867532 doesn't include estimated allele frequencies in the population:

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs61867532

Why might a variant have an rsID number but no estimated allele frequencies for the population based on 1000 genomes project data? Usually when you look up a SNP in dbSNP you can find the estimated allele frequency for the population. 

 

Thanks!

Chloe

ADD COMMENTlink modified 5.1 years ago by rbagnall1.4k • written 5.1 years ago by chloe.p.oconnell80
1
gravatar for rbagnall
5.1 years ago by
rbagnall1.4k
Australia
rbagnall1.4k wrote:

Not all variants in dbSNP have been found in the 1000 Genomes project data. There are countless contributors/projects who have submitted data to dbSNP, and most SNPs are rare.

The variant you indicate was submitted by ENSEMBL from the Watson project, which sequenced the genome of some fella called James Watson. Scroll to the bottom of the page of your link and you will see that this variant was found as a heterozygous change. Most likely this is a rare variant, or perhaps even a sequencing error.

Most variants that you are searching for will not be found in the 1000 Genomes project because you are searching for variants present in less than 1% of the samples in the project.

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by rbagnall1.4k
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