ExAC dataset by GnomAD

Question

[Giulia.cosenza]

Hi everyone, I have a little question. I have a multiple VCF containing variants from 200 people and I wanted to select only the SNPs found in the non-coding regions. So what I did was download from gnomAD the ExAC dataset, which I imagine to be the VCF containing all the SNPs from exomes, and I took off all the position my VCF file had in common with the exome VCF. I found 12 positions, but when I decided to check if they were actually from exomic portions of the human genome I found that they were intronic.

Can anybody explain me haw is this possible?

I attach a pic as example of one of the 12 variant found