SNP annotated outside gene location (Variant Effect Predictor)

Question

[serpalma.v]

I have the following SNP annotated with variant effect predictor to two genes, their locations in the genome are shown as well (UMD3.1):

• rs469441731: chr1:83,591,886-83,591,886
• ENSBTAG00000020106: chr1: 83,583,028-83,591,912 (reverse strand)
• ENSBTAG00000019336: chr1: 83,595,844-83,609,419 (reverse strand)

I see that the location of rs469441731 lies within the boundaries of ENSBTAG00000020106 but not of ENSBTAG00000019336.

I wonder why is rs469441731 annotated to ENSBTAG00000019336

[ATpoint]

Thinking about it quickly, there is the (default) option Upstream/Downstream distance (bp): 5000, which checks the flanking regions of a variant for overlap with a transcripts. As your third range lies within 5kb, maybe that is the reason. Therefore, please provide the full output and the command line used.

Answer 1

[Denise CS]

You need to zoom out to view the boundaries of ENSBTAG00000019336. Variant rs469441731 is 5' UTR with regards to ENSBTAG00000020106, but downstream in regards to ENSBTAG00000019336.

This is the results of the VEP seen on the Location tab of the Ensembl Browser. Note the new data track called 'VEP result' and the variant as a grey box right in the middle of that view. The grey box maps right in the middle of the first exon of ENSBTAG00000020106 (i.e. AP2M1, which is a reverse stranded gene).

You need to zoom out to view a larger region (e.g. 6 kb either side of the SNP of interest), to see the same rs469441731 is downstream of ENSBTAG00000019336 (i.e. DVL3, another reverse stranded gene). This is the zoomed out view.