[ensembl-dev] How can a SNP cause a frameshift mutation

[Andrea Edwards]

Hi

I think I am doing something seriously wrong with the ensembl variation 
database. I have a thousand SNPs which I am looking at, all of which are 
in exons and not a single SNP according to my code is a synonymous or 
non synonymous coding SNP. The vast majority of my SNPs seem to be 
frameshift coding. I don't see how a SNP can cause a frameshift mutation 
- only insertions and deletions can cause that.

I'd be grateful if anyone can see what I am doing wrong

#get adaptors
my $vfa = $reg->get_adaptor($species, 'variation', 'variationfeature');
         my $sa = $reg->get_adaptor($species, 'core', 'slice');
         my $transcript_adaptor =$reg->get_adaptor($species, 
'core','Transcript');

#iterate through my SNPs

while (my $ref = $sth->fetchrow_hashref()) {

         my $slice = $sa->fetch_by_region('chromosome',$ref->{'Chr'});
                 my $new_vf = 
Bio::EnsEMBL::Variation::VariationFeature->new(
                         -start => $ref->{'LiftPos'},  #position of SNP
                         -end => $iLiftPos,
                         -slice => $slice,           # the variation 
must be attached to a slice
                         -allele_string => $iallele,    # the first 
allele should be the reference allele
                         -strand => 1,
                         -map_weight => 1,
                         -adaptor => $vfa,           # we must attach a 
variation feature adaptor
                         -variation_name => 'newSNP',
                     );

             foreach $transcript_variant 
(@{$new_vf->get_all_TranscriptVariations}) {

                     foreach $consequence 
(@{$transcript_variant->consequence_type}) {
                         print "$consequence\n";
                     }
                 }

}

I've stripped the code right down to its minmum as shown above. Not a 
single consequence is synonymous or non synonymous out of 1000 SNPs in 
exons. Plenty of them are intronic but that's to be expected as  SNP 
might be in the exon of one gene but the intron of another.

I'm going to find all the known SNPs in my DNA of interest (cow 
chromosome 7) and see what my code says when ran on known synonymous and 
non-synonymous SNPs.

Any advice or help appreciated

thanks