[ensembl-dev] Allele_num = "?"

[Konrad Karczewski]

Hi Will/VEP team,

Found something unexpected when annotating ExAC with VEP v80. The following variant:

1    139345  .       CGTT    C,TGTT

seems to annotate without error/warnings, but for some of the entries, ALLELE_NUM is `?` - the first few I checked seem to be upstream_gene_variant and the like, so I'm assuming maybe this means both alleles get the same annotation, but I can't find anything in the documentation.

Any information you might have would be very helpful.

Thanks!
-Konrad