Forge Tools gnomad_variant

gnomad_variant read

scidex.forge.gnomad_variant

Look up a variant in gnomAD by chr-pos-ref-alt or rsID. Returns per-population allele frequencies, overall AF, ClinVar significance, and QC flags. Essential for AD/genetics workflows where population gradient matters.

HTTP: POST /api/scidex/forge/gnomad_variant

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.gnomad_variant``.",
  "properties": {
    "variant_id": {
      "anyOf": [
        {
          "maxLength": 64,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "chr-pos-ref-alt variant identifier (e.g. ``19-44908684-T-C`` for APOE rs429358). ``chr`` prefix and ``:`` separator both tolerated. Mutually exclusive with ``rsid``.",
      "title": "Variant Id"
    },
    "rsid": {
      "anyOf": [
        {
          "maxLength": 32,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "dbSNP reference SNP identifier (e.g. ``rs429358``). Mutually exclusive with ``variant_id``. Note: one rsID can map to multiple alleles; the highest-AF record is returned.",
      "title": "Rsid"
    },
    "dataset": {
      "default": "gnomad_r4",
      "description": "gnomAD release. ``gnomad_r4`` (default, v4.1, GRCh38) or ``gnomad_r2_1`` (v2.1.1, GRCh37 — legacy).",
      "title": "Dataset",
      "type": "string"
    }
  },
  "title": "GnomadVariantInput",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "PopulationFrequency": {
      "description": "Per-population allele-count breakdown.\n\nPopulation codes follow gnomAD's short ids: ``nfe`` (non-Finnish\nEuropean), ``afr`` (African / African-American), ``amr``\n(Latino / Admixed American), ``eas`` (East Asian), ``sas``\n(South Asian), ``fin`` (Finnish), ``asj`` (Ashkenazi Jewish),\n``mid`` (Middle Eastern, v4+), ``oth`` (Other).",
      "properties": {
        "population_id": {
          "description": "gnomAD population short code.",
          "title": "Population Id",
          "type": "string"
        },
        "allele_count": {
          "default": 0,
          "description": "Alt-allele observations in this population.",
          "title": "Allele Count",
          "type": "integer"
        },
        "allele_number": {
          "default": 0,
          "description": "Total chromosomes called in this population.",
          "title": "Allele Number",
          "type": "integer"
        },
        "allele_frequency": {
          "default": 0,
          "description": "``allele_count / allele_number`` in ``[0.0, 1.0]``.",
          "title": "Allele Frequency",
          "type": "number"
        },
        "homozygote_count": {
          "default": 0,
          "description": "Homozygotes for the alt allele in this population.",
          "title": "Homozygote Count",
          "type": "integer"
        }
      },
      "required": [
        "population_id"
      ],
      "title": "PopulationFrequency",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.gnomad_variant``.",
  "properties": {
    "variant_id": {
      "description": "Canonical chr-pos-ref-alt id.",
      "title": "Variant Id",
      "type": "string"
    },
    "rsid": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "First dbSNP rsID (``None`` if none).",
      "title": "Rsid"
    },
    "gene_symbol": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Gene symbol from the most-severe consequence.",
      "title": "Gene Symbol"
    },
    "consequence": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Most-severe VEP consequence (e.g. ``missense_variant``).",
      "title": "Consequence"
    },
    "populations": {
      "description": "Per-population allele-count breakdown.",
      "items": {
        "$ref": "#/$defs/PopulationFrequency"
      },
      "title": "Populations",
      "type": "array"
    },
    "overall_af": {
      "default": 0,
      "description": "Overall allele frequency across all populations.",
      "title": "Overall Af",
      "type": "number"
    },
    "clinvar_significance": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "ClinVar clinical-significance string, if any.",
      "title": "Clinvar Significance"
    },
    "flags": {
      "description": "gnomAD QC flags (e.g. ``segdup``, ``lcr``).",
      "items": {
        "type": "string"
      },
      "title": "Flags",
      "type": "array"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "variant_id",
    "took_ms"
  ],
  "title": "GnomadVariantResponse",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/gnomad_variant' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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