Some v4 variants are labeled as intronic when they should be splice region

[mike-w-wilson]

Mark and Konrad found that we have some variants labeled as intron when they should be splice region. The two example variants are https://gnomad.broadinstitute.org/variant/16-30959189-A-G?dataset=gnomad_r4 and https://gnomad.broadinstitute.org/variant/16-30959190-A-G?dataset=gnomad_r4.

Mark noted that the second variant is present in v2 and correctly labeled https://gnomad.broadinstitute.org/variant/16-30970511-A-G?dataset=gnomad_r2_1

I reviewed the v4 release and found that the VEP most_severe_consequence for both variants is splice_donor_region_variant.

Please let me know if you need any more information!