Is there any possibility to predict the specific transcript (obtained by alternative splicing) of a gene present in a particular individual just by exome sequencing and calling variants?
Because we got an analysis report from a recognized institute for an exome sequence we sent which says that they have identified a nucleotide substitution of xxxxx gene, A>G and they have given the transcript ID [ENST00000xxx] as well.
And when I explored further I found this from 1000genomes where they only did exome sequencing but have annotated SNPs with transcript IDs.
http://pilotbrowser.1000genomes.org/...0000323668#ALL
Please could somebody explain this to me? I'm a novice bioinformatician
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nilakshafreezon
On the example from 1000 genomes, if you click on one of the "Show" links, e.g. for "Frameshift coding variants", you'll see exactly how this works. Basically, a single variant can end up getting associated with all of the transcripts that overlap it. So if you have a variant at 5:149720925, then it'll have 4 associated transcripts. These sorts of annotations are mostly for convenience, so you can quickly assess how causative a variant is (if none of the associated transcripts are expressed in your tissue of interest, then the variant is unlikely to be causative).
Thanks for the information. So It's all about the transcripts that overlap with the SNP. :) Thanks again.
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