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Variant Records and Population Frequencies

See the FAQ for dependencies and return conventions.

1) dbSNP variant information

  • Purpose: Retrieve alleles and GRCh37/GRCh38 coordinates for one rsID.
  • Method: Query dbSNP by rsID and retain alleles and assembly coordinates.
  • API: dnakit.annotation.get_dbsnp_variant(rsid[required])
  • Input: An rsID with or without the rs prefix.
  • Output: Returns ProviderResult with query content in data, plus provider and provenance.
  • Example code:
from dnakit.annotation import get_dbsnp_variant

result = get_dbsnp_variant("rs28934578")
print(result.data)
  • Example output: dbSNP coordinates, assembly, and allele records.

2) dbSNP allele frequencies

  • Purpose: Retrieve population allele-frequency records for one rsID.
  • Method: Read dbSNP allele counts and frequencies by study or population.
  • API: dnakit.annotation.get_dbsnp_frequencies(rsid[required])
  • Input: One rsID.
  • Output: Returns ProviderResult with query content in data, plus provider and provenance.
  • Example code:
from dnakit.annotation import get_dbsnp_frequencies

result = get_dbsnp_frequencies("rs28934578")
print(result.data)
  • Example output: Study/population allele-count and frequency records.
  • Purpose: Resolve an rsID or variant query to canonical chrom-pos-ref-alt identifiers.
  • Method: Search the chosen gnomAD dataset for matching variant IDs.
  • API: dnakit.annotation.search_gnomad_variants(query[required], dataset[optional])
  • Input: Query text; DNAKit consistently defaults to gnomad_r4.
  • Output: Returns ProviderResult with query content in data, plus provider and provenance.
  • Example code:
from dnakit.annotation import search_gnomad_variants

result = search_gnomad_variants("rs28934578")
print(result.data)
  • Example output: Matching gnomAD variant IDs and basic metadata.

4) gnomAD aggregate variant data

  • Purpose: Retrieve aggregate frequency data and metadata for one gnomAD variant.
  • Method: Retrieve gnomAD AC, AN and AF by variant ID.
  • API: dnakit.annotation.get_gnomad_variant(variant_id[required], dataset[optional])
  • Input: A chrom-pos-ref-alt identifier; dataset defaults to gnomad_r4.
  • Output: Returns ProviderResult with query content in data, plus provider and provenance.
  • Example code:
from dnakit.annotation import get_gnomad_variant

result = get_gnomad_variant("17-7675088-C-G")
print(result.data)
  • Example output: Aggregate genome/exome allele counts, allele numbers, and frequencies.

5) gnomAD population frequencies

  • Purpose: Retrieve ancestry- and sex-stratified allele frequencies.
  • Method: Extract ancestry/sex-stratified frequencies from the gnomAD variant record.
  • API: dnakit.annotation.get_gnomad_population_frequencies(variant_id[required], dataset[optional])
  • Input: A gnomAD variant ID; dataset defaults to gnomad_r4.
  • Output: Returns ProviderResult with query content in data, plus provider and provenance.
  • Example code:
from dnakit.annotation import get_gnomad_population_frequencies

result = get_gnomad_population_frequencies("17-7675088-C-G")
print(result.data)
  • Example output: AC, AN, and AF values stratified by ancestry and sex.

6) Retrieve dbSNP allele frequencies

  • Purpose: Retrieve dbSNP allele frequencies.
  • Method: Use dbSNPGetFrequencies to query or submit the supplied input and parse the response.
  • API： dnakit.databases.dbsnp_get_frequencies(*, rsid, verbose=True)
  • Input: Provide rsid.
  • Output: Returns a mapping with status, data, rsid, url and related fields.
  • Example code:
import dnakit

result = dnakit.databases.dbsnp_get_frequencies(
    rsid='rs429358',
    verbose=False,
)
print(result)
  • Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "status": "<string>",
  "data": {
    "frequencies": [
      "<object>"
    ],
    "total_studies": "<integer>"
  },
  "rsid": "<string>",
  "url": "<string>"
}

Full parameters and usage notes

7) Retrieve dbSNP coordinates and alleles by rsID

  • Purpose: Retrieve dbSNP coordinates and alleles by rsID.
  • Method: Use dbSNPGetVariantByRsID to query or submit the supplied input and parse the response.
  • API： dnakit.databases.dbsnp_get_variant_by_rsid(*, rsid, verbose=True)
  • Input: Provide rsid.
  • Output: Returns a mapping with status, data, rsid, url and related fields.
  • Example code:
import dnakit

result = dnakit.databases.dbsnp_get_variant_by_rsid(
    rsid='rs12345',
    verbose=False,
)
print(result)
  • Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "status": "<string>",
  "data": {
    "refsnp_id": "<string>",
    "snp_id": "<integer>",
    "chromosome": "<string>",
    "position": "<string>",
    "assembly": "<string>",
    "position_grch38": "<string>",
    "position_grch37": "<string>",
    "allele": "<string>"
  },
  "rsid": "<string>",
  "url": "<string>"
}

Full parameters and usage notes

8) Retrieve gnomAD gene constraint metrics

  • Purpose: Retrieve gnomAD gene constraint metrics.
  • Method: Use gnomADGetGeneConstraints to query or submit the supplied input and parse the response.
  • API： dnakit.databases.gnomad_get_gene_constraints(*, gene_symbol, reference_genome=None, verbose=True)
  • Input: Provide gene_symbol.
  • Output: Returns a mapping with gene, note and related fields.
  • Example code:
import dnakit

result = dnakit.databases.gnomad_get_gene_constraints(
    gene_symbol='BRCA1',
    reference_genome='GRCh38',
    verbose=False,
)
print(result)
  • Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "gene": {
    "symbol": "<string>",
    "gene_id": "<string>",
    "exac_constraint": "<object>",
    "gnomad_constraint": {
      "exp_lof": "<number>",
      "obs_lof": "<integer>",
      "oe_lof": "<number>",
      "pLI": "<number>",
      "exp_mis": "<number>",
      "obs_mis": "<integer>",
      "oe_mis": "<number>",
      "exp_syn": "<number>"
    },
    "mitochondrial_constraint": "<object>"
  },
  "note": "<string>"
}

Full parameters and usage notes

9) Retrieve gnomAD variant metadata

  • Purpose: Retrieve gnomAD variant metadata.
  • Method: Use gnomADGraphQLQuery to query or submit the supplied input and parse the response.
  • API： dnakit.databases.gnomad_get_variant(*, variant_id, dataset=None, verbose=True)
  • Input: Provide variant_id.
  • Output: Returns a mapping with variant, dataset, reference_genome, dataset_note and related fields.
  • Example code:
import dnakit

result = dnakit.databases.gnomad_get_variant(
    variant_id='19-44908822-C-T',
    dataset='gnomad_r3',
    verbose=False,
)
print(result)
  • Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "variant": {
    "variant_id": "<string>",
    "chrom": "<string>",
    "pos": "<integer>",
    "ref": "<string>",
    "alt": "<string>",
    "rsid": "<string>",
    "genome": {
      "af": "<number>",
      "an": "<integer>",
      "ac": "<integer>"
    },
    "exome": {
      "af": "<number>",
      "an": "<integer>",
      "ac": "<integer>"
    }
  },
  "dataset": "<string>",
  "reference_genome": "<string>",
  "dataset_note": "<string>"
}

Full parameters and usage notes

10) Retrieve ancestry-specific gnomAD allele frequencies

  • Purpose: Retrieve ancestry-specific gnomAD allele frequencies.
  • Method: Use gnomADGetVariantPopulations to query or submit the supplied input and parse the response.
  • API： dnakit.databases.gnomad_get_variant_populations(*, variant_id, dataset=None, verbose=True)
  • Input: Provide variant_id.
  • Output: Returns a mapping with variant_id, chrom, pos, ref and related fields.
  • Example code:
import dnakit

result = dnakit.databases.gnomad_get_variant_populations(
    variant_id='1-55051215-G-GA',
    dataset='gnomad_r4',
    verbose=False,
)
print(result)
  • Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "variant_id": "<string>",
  "chrom": "<string>",
  "pos": "<integer>",
  "ref": "<string>",
  "alt": "<string>",
  "rsid": "<string>",
  "dataset": "<string>",
  "genome": {
    "ac": "<integer>",
    "an": "<integer>",
    "af": "<number>",
    "populations": [
      "<object>"
    ]
  }
}

Full parameters and usage notes

11) Search gnomAD variant identifiers

  • Purpose: Search gnomAD variant identifiers.
  • Method: Use gnomADGraphQLQuery to query or submit the supplied input and parse the response.
  • API： dnakit.databases.gnomad_search_variants(*, query=None, dataset=None, variant=None, verbose=True)
  • Input: Choose filters as shown in the example; omitted options use the operation defaults.
  • Output: Returns a mapping with variant_search, dataset, reference_genome, dataset_note and related fields.
  • Example code:
import dnakit

result = dnakit.databases.gnomad_search_variants(
    query='rs7412',
    dataset='gnomad_r3',
    verbose=False,
)
print(result)
  • Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "variant_search": [
    {
      "variant_id": "<string>"
    }
  ],
  "dataset": "<string>",
  "reference_genome": "<string>",
  "dataset_note": "<string>"
}

Full parameters and usage notes