Help needed understanding VEP: Allele - the variant allele used to calculate the consequence

Question

[velan]

Hi,

Could somebody please explain me how this Allele column is computed in EnsEMBL VEP (Variant Effect Predictor)

Sample VEP output

#Uploaded_variation Location Allele Gene Feature ...

T Y:2652175 0:0 ENSG00000223773 ENST00000435581 Transcript intron_variant -/2788
T Y:2652175 6:124 - ENSR00001555882 RegulatoryFeature

I am thinking of filtering the results based on this Allele, since there are significant amount of position has 0:0. Some places the values are very high. The documentation only says

Allele - the variant allele used to calculate the consequence Thanks in advance.

[Emily]

What was your input? The Allele column should display your alternative allele, so something like G or - or duplication.