regulatory_region_variant not reported in SnpEff annotation

usegalaxy.eu support
,
1

Hello everyone,

I annotated my sequencing data with SnpEff ( SnpEff eff: annotate variants (Galaxy Version 4.3+T.galaxy1)) using the database SnpEff download: SnpEff4.3 GRCh37.75 ( SnpEff download: download a pre-built database (Galaxy Version 4.3+T.galaxy2)).
When checking some variants, I found that information regarding regulatory region variants are not supplied (as they are using the VEP for Ensemble version 75). Does the SnpEff database generally not supply this information?

Thanks!

All the best,
Rose

Example: 9_139400219_G/A

SnpEff annotation
A|missense_variant|MODERATE|NOTCH1|ENSG00000148400|transcript|ENST00000277541|protein_coding|25/34|c.4129C>T|p.Pro1377Ser|4205/9371|4129/7668|1377/2555||,A|upstream_gene_variant|MODIFIER|NOTCH1|ENSG00000148400|transcript|ENST00000494783|processed_transcript||n.-922C>T|||||922|

output VEP see picture attached

Bildschirmfoto 2020-05-04 um 22.40.34
Bildschirmfoto 2020-05-04 um 22.40.341047×273 45 KB

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
9_139400219_G/A 9:139400219 A ENSG00000148400 ENST00000494783 Transcript upstream_gene_variant - - - - - rs61751542 STRAND=-1;SYMBOL=NOTCH1;DISTANCE=922;SYMBOL_SOURCE=HGNC;GMAF=A:0.0087236
9_139400219_G/A 9:139400219 A - ENSR00001317600 RegulatoryFeature regulatory_region_variant - - - - - rs61751542 GMAF=A:0.0087236
9_139400219_G/A 9:139400219 A ENSG00000148400 ENST00000277541 Transcript missense_variant 4205 4129 1377 P/S Ccc/Tcc rs61751542 ENSP=ENSP00000277541;STRAND=-1;SYMBOL=NOTCH1;HGVSc=ENST00000277541.6:c.4129C>T;HGVSp=ENSP00000277541.6:p.Pro1377Ser;SYMBOL_SOURCE=HGNC;GMAF=A:0.0087236
2

I would be glad for any help! Thanks a lot! Rose

3

Hi @roselucia,

this is a good question.
SnpEff has a regulatory_region_variant effect, but regulatory effects belong to the additional annotations described in chapter 6 of the SnpEff manual, which you have to enable explicitly.
In the Galaxy wrapper, this is hidden in the section Regulation options just below the SnpEff4.3 Genome Data select box if you want to use it.

Best,
Wolfgang

2 Likes