Gnomad Database

import requests

def query_gnomad_gene(gene_symbol, dataset="gnomad_r4", reference_genome="GRCh38"):
    """Fetch variants in a gene from gnomAD."""
    url = "https://gnomad.broadinstitute.org/api"

    query = """
    query GeneVariants($gene_symbol: String!, $dataset: DatasetId!, $reference_genome: ReferenceGenomeId!) {
      gene(gene_symbol: $gene_symbol, reference_genome: $reference_genome) {
        gene_id
        gene_symbol
        variants(dataset: $dataset) {
          variant_id
          pos
          ref
          alt
          consequence
          genome {
            af
            ac
            an
            ac_hom
            populations {
              id
              ac
              an
              af
            }
          }
          exome {
            af
            ac
            an
            ac_hom
          }
          lof
          lof_flags
          lof_filter
        }
      }
    }
    """

    variables = {
        "gene_symbol": gene_symbol,
        "dataset": dataset,
        "reference_genome": reference_genome
    }

    response = requests.post(url, json={"query": query, "variables": variables})
    return response.json()

# Example
result = query_gnomad_gene("BRCA1")
gene_data = result["data"]["gene"]
variants = gene_data["variants"]

# Filter to rare PTVs
rare_ptvs = [
    v for v in variants
    if v.get("lof") == "LC" or v.get("consequence") in ["stop_gained", "frameshift_variant"]
    and v.get("genome", {}).get("af", 1) < 0.001
]
print(f"Found {len(rare_ptvs)} rare PTVs in {gene_data['gene_symbol']}")

import requests

def query_gnomad_variant(variant_id, dataset="gnomad_r4"):
    """Fetch details for a specific variant (e.g., '1-55516888-G-GA')."""
    url = "https://gnomad.broadinstitute.org/api"

    query = """
    query VariantDetails($variantId: String!, $dataset: DatasetId!) {
      variant(variantId: $variantId, dataset: $dataset) {
        variant_id
        chrom
        pos
        ref
        alt
        genome {
          af
          ac
          an
          ac_hom
          populations {
            id
            ac
            an
            af
          }
        }
        exome {
          af
          ac
          an
          ac_hom
          populations {
            id
            ac
            an
            af
          }
        }
        consequence
        lof
        rsids
        in_silico_predictors {
          id
          value
          flags
        }
        clinvar_variation_id
      }
    }
    """

    response = requests.post(
        url,
        json={"query": query, "variables": {"variantId": variant_id, "dataset": dataset}}
    )
    return response.json()

# Example: query a specific variant
result = query_gnomad_variant("17-43094692-G-A")  # BRCA1 missense
variant = result["data"]["variant"]

if variant:
    genome_af = variant.get("genome", {}).get("af", "N/A")
    exome_af = variant.get("exome", {}).get("af", "N/A")
    print(f"Variant: {variant['variant_id']}")
    print(f"  Consequence: {variant['consequence']}")
    print(f"  Genome AF: {genome_af}")
    print(f"  Exome AF: {exome_af}")
    print(f"  LoF: {variant.get('lof')}")

import requests

def query_gnomad_constraint(gene_symbol, reference_genome="GRCh38"):
    """Fetch constraint scores for a gene."""
    url = "https://gnomad.broadinstitute.org/api"

    query = """
    query GeneConstraint($gene_symbol: String!, $reference_genome: ReferenceGenomeId!) {
      gene(gene_symbol: $gene_symbol, reference_genome: $reference_genome) {
        gene_id
        gene_symbol
        gnomad_constraint {
          exp_lof
          exp_mis
          exp_syn
          obs_lof
          obs_mis
          obs_syn
          oe_lof
          oe_mis
          oe_syn
          oe_lof_lower
          oe_lof_upper
          lof_z
          mis_z
          syn_z
          pLI
        }
      }
    }
    """

    response = requests.post(
        url,
        json={"query": query, "variables": {"gene_symbol": gene_symbol, "reference_genome": reference_genome}}
    )
    return response.json()

# Example
result = query_gnomad_constraint("KCNQ2")
gene = result["data"]["gene"]
constraint = gene["gnomad_constraint"]

print(f"Gene: {gene['gene_symbol']}")
print(f"  pLI:   {constraint['pLI']:.3f}  (>0.9 = LoF intolerant)")
print(f"  LOEUF: {constraint['oe_lof_upper']:.3f}  (<0.35 = highly constrained)")
print(f"  Obs/Exp LoF: {constraint['oe_lof']:.3f}")
print(f"  Missense Z:  {constraint['mis_z']:.3f}")

import requests
import pandas as pd

def get_population_frequencies(variant_id, dataset="gnomad_r4"):
    """Extract per-population allele frequencies for a variant."""
    url = "https://gnomad.broadinstitute.org/api"

    query = """
    query PopFreqs($variantId: String!, $dataset: DatasetId!) {
      variant(variantId: $variantId, dataset: $dataset) {
        variant_id
        genome {
          populations {
            id
            ac
            an
            af
            ac_hom
          }
        }
      }
    }
    """

    response = requests.post(
        url,
        json={"query": query, "variables": {"variantId": variant_id, "dataset": dataset}}
    )
    data = response.json()
    populations = data["data"]["variant"]["genome"]["populations"]

    df = pd.DataFrame(populations)
    df = df[df["an"] > 0].copy()
    df["af"] = df["ac"] / df["an"]
    df = df.sort_values("af", ascending=False)
    return df

# Population IDs in gnomAD v4:
# afr = African/African American
# ami = Amish
# amr = Admixed American
# asj = Ashkenazi Jewish
# eas = East Asian
# fin = Finnish
# mid = Middle Eastern
# nfe = Non-Finnish European
# sas = South Asian
# remaining = Other

import requests

def query_gnomad_sv(gene_symbol):
    """Query structural variants overlapping a gene."""
    url = "https://gnomad.broadinstitute.org/api"

    query = """
    query SVsByGene($gene_symbol: String!) {
      gene(gene_symbol: $gene_symbol, reference_genome: GRCh38) {
        structural_variants {
          variant_id
          type
          chrom
          pos
          end
          af
          ac
          an
        }
      }
    }
    """

    response = requests.post(url, json={"query": query, "variables": {"gene_symbol": gene_symbol}})
    return response.json()