Forge Tools clinvar_variant

clinvar_variant read

scidex.forge.clinvar_variant

Look up variants in NCBI ClinVar by gene symbol, HGVS expression, or variation ID. Returns clinical significance (Pathogenic/VUS/Benign), ACMG review status (0–4 stars), associated disease conditions, and submitter count. Complements gnomad_variant with clinical interpretations.

HTTP: POST /api/scidex/forge/clinvar_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.clinvar_variant``.",
  "properties": {
    "variant_id": {
      "anyOf": [
        {
          "maxLength": 64,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "ClinVar variation ID (numeric, e.g. ``12375``) or VCV/RCV accession (e.g. ``VCV000012375``). At least one of ``variant_id``, ``gene_symbol``, or ``hgvs`` is required.",
      "title": "Variant Id"
    },
    "gene_symbol": {
      "anyOf": [
        {
          "maxLength": 64,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "HGNC gene symbol (e.g. ``BRCA1``, ``CFTR``). Returns all ClinVar variants annotated to this gene, up to ``limit``.",
      "title": "Gene Symbol"
    },
    "hgvs": {
      "anyOf": [
        {
          "maxLength": 256,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "HGVS expression (e.g. ``NM_007294.4:c.5266dupC``). ClinVar accepts standard HGVS notation for transcript or genomic variants.",
      "title": "Hgvs"
    },
    "clinical_significance": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional significance filter. Only variants whose clinical significance contains at least one of these strings (case-insensitive) are returned. Common values: ``Pathogenic``, ``Likely pathogenic``, ``Uncertain significance``, ``Likely benign``, ``Benign``.",
      "title": "Clinical Significance"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of variants to return (default 20, max 200).",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeClinVarIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "ClinVarVariantOut": {
      "description": "One ClinVar variant in the response.",
      "properties": {
        "variation_id": {
          "description": "ClinVar numeric variation ID.",
          "title": "Variation Id",
          "type": "string"
        },
        "accession": {
          "default": "",
          "description": "ClinVar VCV accession (e.g. ``VCV000012375.35``).",
          "title": "Accession",
          "type": "string"
        },
        "title": {
          "default": "",
          "description": "Variant title from ClinVar.",
          "title": "Title",
          "type": "string"
        },
        "gene_symbol": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Primary gene symbol for this variant.",
          "title": "Gene Symbol"
        },
        "clinical_significance": {
          "default": "",
          "description": "Clinical significance string (e.g. ``Pathogenic``, ``Uncertain significance``, ``Benign``).",
          "title": "Clinical Significance",
          "type": "string"
        },
        "review_status": {
          "default": "",
          "description": "Human-readable ClinVar review status.",
          "title": "Review Status",
          "type": "string"
        },
        "review_stars": {
          "default": 0,
          "description": "0–4 star review level per ACMG/AMP evidence tiers (0=no assertion, 4=practice guideline).",
          "maximum": 4,
          "minimum": 0,
          "title": "Review Stars",
          "type": "integer"
        },
        "condition_names": {
          "description": "Associated disease/condition names.",
          "items": {
            "type": "string"
          },
          "title": "Condition Names",
          "type": "array"
        },
        "submitter_count": {
          "default": 0,
          "description": "Number of SCV submissions supporting this classification.",
          "minimum": 0,
          "title": "Submitter Count",
          "type": "integer"
        },
        "last_evaluated": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Date last evaluated (YYYY-MM-DD), or None.",
          "title": "Last Evaluated"
        }
      },
      "required": [
        "variation_id"
      ],
      "title": "ClinVarVariantOut",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.clinvar_variant``.",
  "properties": {
    "variants": {
      "description": "Matching ClinVar variants, ordered by ClinVar's relevance ranking.",
      "items": {
        "$ref": "#/$defs/ClinVarVariantOut"
      },
      "title": "Variants",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total variants matching the query before the ``limit`` was applied. May exceed ``len(variants)``.",
      "title": "Total Found",
      "type": "integer"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream calls.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "took_ms"
  ],
  "title": "ForgeClinVarOut",
  "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/clinvar_variant' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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