Hi all,
I have some doubts regarding the EXAC (Exome Aggregation Consortium) dataset. For a gene, if we click a variant it gives a detailed description about that particular variant. What does non coding transcript exon under Annotations mean?. And when you move the cursor to the allele number it shows total number of called genotypes. Does it refer to the depth to which it is sequenced? and what does site quality metrics mean?. Thank you.
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As you can see, that variant is localized in 4 transcripts. The annotation is a missense variant for 3 transcripts of that gene and the fourth transcript is a noncoding transcript (i.e. it has no known protein product). As such the annotation is for the fourth that this variant is localized in an exon of a non coding transcript. You can see this gene in Ensembl: http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000198959;r=20:38128461-38133760;t=ENST00000469269 And indeed, there are both coding and non-coding transcripts.
Thank you so much. Now its clear for me. If you dont mind I have one more query. Under Population Frequencies there is allele count and allele number. But for some populations the allele count is 0 but there is allele number. Does it mean that particular variant is absent in that population. For example in this link below there are 2 carriers in European and 1 in African. Although in other populations its 0 carriers there are allele numbers.
http://exac.broadinstitute.org/variant/20-36758625-G-A
The allele count is the number of times that variant was found, the allele number is the number of alleles that have been sequenced. So for your example variant: In the European (Non-Finnish) population the variant is found twice out of 62648 alleles (and thus 31324 individuals). In the East Asian population the variant is not found (0) out of 8084 alleles (and thus 4042 individuals).
Do you mean that out of 31324 sequenced European (Non-Finnish) individuals only 2 had this variant?
Yes indeed. See also the very low allele frequency in the last column (3.192e-05).
Thank you so much for your time.