Hi,
I downloaded the base-level pext TSV file. However, I’m a bit confused because the base coordinates don’t seem to match. For example, the gene ENSG00000007866 has coordinates 6:35473597-35497079, but in the TSV file, the locus for the same gene spans 6:35442821–6:35454439.
> zgrep '^ENSG00000007866' all.baselevel.021620.tsv.bgz | cut -f1,2 | awk 'NR==1 {first=$0} {last=$0} END {print first; print last}'
ENSG00000007866 6:35442821
ENSG00000007866 6:35454439
I hope my questions make sense, thank you in advance for your help!
Update:
It appears that the base-level pext TSV file (from the v4 download section) agrees with the GRCh37 assembly annotations, not GRCh38, which I believe is the reference used in gnomAD v4. This would explain the coordinate mismatch.