cyberneticlibrary
← library

Query population variant frequencies and constraints

gnomad-variantsskillsetup L2★35
ammawla/encode-toolkit ↗
What it does

Query gnomAD for variant frequencies and gene constraint scores

Best for

Filtering ENCODE regulatory variants by population rarity and assessing gene constraint before functional validation

Inputs
  • · variant ID (rs or chr-pos-ref-alt)
  • · gene symbol
  • · genomic region
Outputs
  • · allele frequencies
  • · LOEUF/pLI scores
  • · population-specific AF
Requires
  • · gnomAD GraphQL API
Preconditions

None; no authentication required

Failure modes
  • · Variant not present in gnomAD (ultra-rare)
  • · Outdated pLI scores (legacy metric)
  • · Region queries returning incomplete results
Trust signals
  • · gnomAD v4.1 (807K individuals)
  • · Karczewski et al 2020 citation
  • · LOEUF threshold guidance