Update gnomad v4.1 sub populations in relevant places

[nakib103]

We have updated gnomAD to v4.1 - https://www.ebi.ac.uk/panda/jira/browse/ENSVAR-6286

It has two sub-population name updates -

• gnomade oth --> gnomade remaining
• gnomadg oth --> gnomadg remaining

And one new sub population -

• gnomade mid

This change needs to be reflected where we have this information stored in VEP -

• in Constants.pm where we define fields and their header description
• in OutFactory.pm and OutputFactory/JSON.pm where we put what fields to expect from gnomad frequency

Test

REST

grch38 -
genomes - http://wp-np2-11:7075/vep/human/id/rs1603308226?content-type=application/json
exomes - http://wp-np2-11:7075/vep/human/id/rs2124485780?content-type=application/json

grch37 -
genomes - http://wp-np2-11:7075/vep/human/id/rs7892850?content-type=application/json
exomes - http://wp-np2-11:7075/vep/human/id/rs2124485742?content-type=application/json

CLI

vep --id "Y 2781716 rs1603308226 T C" --cache <cache_dir> --fasta <fasta> --offline --force --everything

[likhitha-surapaneni]

Works as expected for grch37 and grch38. Thanks @nakib103

[nakib103]

merged to main and release/113