What is the GENCODE version for the constraint metrics file

General
1

Hi,
In the current help page for constraint metrics, it is mentioned GENCODE v39 as the reference for transcripts from protein coding genes. I have two questions,

  1. The file actually present ensembl transcript identifiers. Are those identifiers retrieve directly from the GENCODE rather than EnsEMBL?
  2. What source of transcript (and their identifers) was used for the constraint metrics of GnomAD 2.1.1 and for GnomAD v.4.0/v.4.1? Are the same version for both? Thank you.

Best,
Javier

2

Hi Javier,

Transcript identifiers come from GENCODE and are added to our data when we run VEP. gnomAD v4 was annotated with VEP version 105 using GENCODE v39, and gnomAD v2 was annotated with VEP version 85 using GENCODE v19.

Regards,
Kristen