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

[Andrea Edwards]

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