[ensembl-dev] nsSNP difference between script and website

[tjaart at ebi.ac.uk]

Hi guys

I am trying to get the non_synonymous snps associated with a specific
human transcript. Until version 59 of Ensembl the following script worked:

#!/usr/bin/perl -w
use strict;
use warnings;
use Bio::EnsEMBL::Registry;
use Getopt::Long;

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
    -host => 'ensembldb.ensembl.org',
    -user => 'anonymous',
);

&GetOptions('trans:s' => \my $trans);

my $stable_id =$trans;
my $transcript_adaptor = $registry->get_adaptor('homo sapiens', 'core',
'transcript');
my $transcript = $transcript_adaptor->fetch_by_stable_id($stable_id);

my $trv_adaptor = $registry->get_adaptor('homo sapiens', 'variation',
'transcriptvariation');
my $trvs = $trv_adaptor->fetch_all_by_Transcripts([$transcript]);

foreach my $tv (@{$trvs})
{
	my $cons = join(",",@{$tv->consequence_type});
	if ($cons =~ /NON_SYNONYMOUS_CODING/)
	{
		print $tv->translation_start()," ";
		print $tv->pep_allele_string();
		print "\n";
	}
}

When running it this morning I get results that differ from the current
Ensembl website.

For transcript ENST00000466254 I get the following variants using my script:

NON_SYNONYMOUS_CODING 37 Y/F rs1042956
NON_SYNONYMOUS_CODING 104 S/L rs61732509
NON_SYNONYMOUS_CODING 117 V/F rs56261425

When looking at the webpage
(http://www.ensembl.org/Homo_sapiens/Transcript/ProtVariations?db=core;g=ENSG00000211772;r=7:142498725-142500432;t=ENST00000466254)
I get 9 nsSNPs, none of which correspond to my nsSNPs:

37 	rs1042956 	Non-synonymous 	A/T 	W 	S, T
38 	rs1042957 	Non-synonymous 	C/T 	Y 	P, L
57 	rs61732510 	Non-synonymous 	C/T 	Y 	A, V
58 	rs1042959 	Non-synonymous 	A/G 	R 	Q, R
60 	rs1062612 	Non-synonymous 	G/A 	R 	H, R
80 	rs60112268 	Non-synonymous 	A/C 	M 	C, *
104 	rs61732509 	Non-synonymous 	C/T 	Y 	W, R
116 	rs56261425 	Non-synonymous 	G/T 	YK 	P, L
160 	rs1042966 	Non-synonymous 	C/T 	Y 	P, L

The dbSNP ids are present in the page but the amino acid changes differ
from what I get with my script.

Am I making an error somewhere in my script? I did upgrade the API as well
to the latest version (60).

Hope you guys can help.

Tjaart