[ensembl-dev] why would a snp have multiple consequences in the same transcript

[Graham Ritchie]

Hi Andrea,

You are correct that sometimes consequences are not mutually exclusive (as per your example with a codon change and splice region), so that means we need to return a list of consequences. You can get the single consequence that we consider the 'worst' by using the display_consequence method on a TranscriptVariation object.

Another potential source of confusion is that the variation associated with the transcript_variation may have more than one alternative allele, each of which may have a different effect on the transcript (e.g. the A allele from a variation like G/A/T could be synonymous while the T could be non-synonymous). Our current schema cannot store this information and we are currently working on a revised schema which will explicitly link alleles to their consequences, but this will still be a many to one relationship to allow for non-mutually exclusive consequence types.

Hope that makes sense, if you have any further questions just ask. 

Cheers,

Graham

Ensembl variation


On 19 Nov 2010, at 15:22, Andrea Edwards wrote:

> Hi
> 
> I think I have asked this question before but I can't find the answer in my archive of answers so I'm really really sorry about this.
> 
> Why would a SNP have multiple consequences in a single transcript?  This code returns an array of consequences:
> 
> my @tvs = @{$vf->get_all_TranscriptVariations};
> foreach my $tv (@tvs) {
>    my @consequences = @{$tv->consequence_type};
> 
> where $vf is a variation feature and $tv is a transcript variant.
> 
> I thought perhaps this could be a convention issue with the api as you generally return array references from functions
> 
> I understand a SNP could have different consequences in the same gene as it might have a different impact on each splice variant, but how can it have multiple consequences in a single transcript?
> 
> I've looked at the consequence types and they do appear to be mutually exclusive. At best something could be both synonymous and  splice site (or non-syn and  splice site) if it occurs in the first/last few bases of an exon
> 
> I apologise for the duplicate question.
> 
> Thanks in advance for your help
> 
> 
> 
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