<p>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?<br />
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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&gt;G and they have given the transcript ID [ENST00000xxx] as well.<br />
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And when I explored further I found this from 1000genomes where they only did exome sequencing but have annotated SNPs with transcript IDs.<br />
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<a href="http://pilotbrowser.1000genomes.org/Homo_sapiens/Gene/Variation_Gene/Table?db=core;g=ENSG00000070814;r=5:149717428-149740111;t=ENST00000323668#ALL" target="_blank">http://pilotbrowser.1000genomes.org/...0000323668#ALL</a><br />
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Please could somebody explain this to me? I&#39;m a novice bioinformatician</p>

<p>On the example from 1000 genomes, if you click on one of the &quot;Show&quot; links, e.g. for &quot;Frameshift coding variants&quot;, you&#39;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&#39;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).</p>
