[ensembl-dev] Understanding VEP Rest output

[Wolf Beat]

Hi, i have a question out the minor_allele field of the colocated_variants field in the VEP response.


for rs351771 (G>A) i don't fully understand the logic of the answer:


http://rest.ensembl.org/vep/hsapiens/id/rs351771?ExAC=1&content-type=application/json


What i have trouble understanding is the minor_allele for 1000 genomes (thats minor_allele i think) and for the others.

For all, except minor_alelle, the minor allele is "A". But for minor_allele its "G".


>From what i can guess, the variant is a little borderline between a variant and a false reference, meaning, the reference sequence might actually be the minor_allele.


But what i don't understand are the numbers from gnomad etc. reported by VEP. If i read the http://gnomad.broadinstitute.org/variant/5-112164561-G-A website correctly, the frequency of A should be quite high, 50%+. Yet VEP tells me that the frequency of A in gnomad is way under 1%.


Am I missing something here? Can somebody help me to better understand the output of VEP?


Kind regards


Beat Wolf