[ensembl-dev] VEP perl script vs web

[Sung Gong]

Hi,

Thanks for developing VEP and make it available to the public.

I found some discrepancies between the web version of VEP and the perl
script for the data shown below:
Chr Start End Allele
1       6264301 6264301 A/G

>From the web version, it returns eight entries which are shown below:

Uploaded Variation	Location	Allele	Gene	Feature	Feature
type	Consequence	Position in cDNA	Position in CDS	Position in
protein	Amino acid change	Codon change	Co-located Variation	Extra
1_6264301_A/G	1:6264301-6264302	A	ENSG00000116251	ENST00000462296	Transcript	UPSTREAM	-	-	-	-	-	-	-
1_6264301_A/G	1:6264301-6264302	A	ENSG00000158286	ENST00000377948	Transcript	UPSTREAM	-	-	-	-	-	-	-
1_6264301_A/G	1:6264301-6264302	A	ENSG00000116251	ENST00000471204	Transcript	WITHIN_NON_CODING_GENE,INTRONIC	-	-	-	-	-	-	-
1_6264301_A/G	1:6264301-6264302	G	ENSG00000158286	ENST00000485539	Transcript	UPSTREAM	-	-	-	-	-	-	-
1_6264301_A/G	1:6264301-6264302	A	ENSG00000158286	ENST00000466994	Transcript	UPSTREAM	-	-	-	-	-	-	-
1_6264301_A/G	1:6264301-6264302	G	ENSG00000116251	ENST00000234875	Transcript	UPSTREAM	-	-	-	-	-	-	-
1_6264301_A/G	1:6264301-6264302	G	ENSG00000158286	ENST00000377948	Transcript	UPSTREAM	-	-	-	-	-	-	-
1_6264301_A/G	1:6264301-6264302	A	ENSG00000116251	ENST00000234875	Transcript	UPSTREAM	-	-	-	-	-	-	-

However, using the perl script, the same position is mapped onto 14
Ensembl transcript as shown below:

1_6264301_A/G   1:6264301   G   ENSG00000116251 ENST00000465387
Transcript  UPSTREAM    -   -   -   -   -   -   -
1_6264301_A/G   1:6264301   G   ENSG00000226944 ENST00000455744
Transcript  DOWNSTREAM  -   -   -   -   -   -   -
1_6264301_A/G   1:6264301   G   ENSG00000116251 ENST00000234875
Transcript  UPSTREAM    -   -   -   -   -   -   -
1_6264301_A/G   1:6264301   G   ENSG00000158286 ENST00000377939
Transcript  UPSTREAM    -   -   -   -   -   -   -
1_6264301_A/G   1:6264301   G   ENSG00000116251 ENST00000497965
Transcript  UPSTREAM    -   -   -   -   -   -   -
1_6264301_A/G   1:6264301   G   ENSG00000158286 ENST00000485539
Transcript  UPSTREAM    -   -   -   -   -   -   -
1_6264301_A/G   1:6264301   G   ENSG00000158286 ENST00000484435
Transcript  UPSTREAM    -   -   -   -   -   -   -
1_6264301_A/G   1:6264301   G   ENSG00000116251 ENST00000480661
Transcript  UPSTREAM    -   -   -   -   -   -   -
1_6264301_A/G   1:6264301   G   ENSG00000158286 ENST00000377948
Transcript  UPSTREAM    -   -   -   -   -   -   -
1_6264301_A/G   1:6264301   G   ENSG00000116251 ENST00000462296
Transcript  UPSTREAM    -   -   -   -   -   -   -
1_6264301_A/G   1:6264301   G   ENSG00000158286 ENST00000466994
Transcript  UPSTREAM    -   -   -   -   -   -   -
1_6264301_A/G   1:6264301   G   ENSG00000116251 ENST00000471204
Transcript  WITHIN_NON_CODING_GENE,INTRONIC -   -   -   -   -   -   -
1_6264301_A/G   1:6264301   G   ENSG00000158286 ENST00000496676
Transcript  UPSTREAM    -   -   -   -   -   -   -
1_6264301_A/G   1:6264301   G   ENSG00000116251 ENST00000465335
Transcript  WITHIN_NON_CODING_GENE,INTRONIC -   -   -   -   -   -   -

Strangely, the Ensembl gene, ENSG00000226944, from the second entry
above is not even shown from the web version of VEP. Also, there are
two allele types (A and G) from the web version whereas G from the
perl script.
In addition, the position which I queried (chr1:6264301-6264301) only
belongs to the chromosome location of ENSG00000116251 amongst the
three Ensembl gene identifiers (ENSG00000116251, ENSG00000226944, and
ENSG00000158286) - see below:
http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Gene;end=1;q=ENSG00000116251
http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Gene;end=1;q=ENSG00000226944
http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Gene;end=2;q=ENSG00000158286

Did I miss something?
Any help?

Cheers,
Sung