Server definition
- Hash
- sha256:14222822b535bc33580aa4aee2cc0fc3757a2e423ebca48884fe527866eb2a43
- What it is
- What a remote MCP server returned when asked what it offers: 7 tools
The blob, as servednamed by its sha256
{
"instructions": "Population genetics over gnomAD. dataset (gnomad_r4 default, GRCh38) and reference_genome are distinct, coherent parameters — keep the build aligned with ensembl coordinates; both are echoed in output. Per-ancestry allele frequencies are never collapsed to a single global AF. An absent variant is uninterpretable without gnomad_get_coverage — confirm the position is callable before concluding true absence (the gnomad_variant_triage prompt chains this). gnomad_list_gene_variants and gnomad_search_clinvar stage results too large to inline on a DataCanvas (set CANVAS_PROVIDER_TYPE=duckdb) — inspect the staged table with gnomad_dataframe_describe, then query it with gnomad_dataframe_query. The gnomAD API is community-funded and rate-limited — calls are concurrency-capped and back off.\nData source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/",
"tools": [
{
"description": "List the tables staged on a canvas and their columns (name and type) so you can write correct SQL for gnomad_dataframe_query. Use the canvas_id returned by gnomad_list_gene_variants or gnomad_search_clinvar. Returns one entry per table with its row count and column schema.",
"inputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"properties": {
"canvas_id": {
"description": "Canvas ID returned by a prior staging call (gnomad_list_gene_variants or gnomad_search_clinvar).",
"pattern": "^[A-Za-z0-9_-]{10}$",
"type": "string"
}
},
"required": [
"canvas_id"
],
"type": "object"
},
"name": "gnomad_dataframe_describe",
"outputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"tables"
]
},
{
"required": [
"error"
]
}
],
"properties": {
"error": {
"additionalProperties": {},
"description": "Present when the call failed. Absent on success.",
"properties": {
"code": {
"description": "JSON-RPC error code for this failure.",
"maximum": 9007199254740991,
"minimum": -9007199254740991,
"type": "integer"
},
"data": {
"additionalProperties": {},
"properties": {
"reason": {
"description": "Machine-readable failure mode. Declared by this tool: `canvas_disabled`: DataCanvas is not enabled on this server instance. Other values are possible when a failure originates below the handler.",
"examples": [
"canvas_disabled"
],
"type": "string"
},
"recovery": {
"additionalProperties": {},
"description": "Actionable next step for the caller.",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"type": "object"
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"type": "object"
},
"message": {
"description": "Human-readable description of what went wrong.",
"type": "string"
}
},
"required": [
"code",
"message"
],
"type": "object"
},
"tables": {
"description": "Tables staged on the canvas.",
"items": {
"additionalProperties": false,
"description": "One staged table: name, row count, and column schema.",
"properties": {
"columns": {
"description": "Column schema, in order.",
"items": {
"additionalProperties": false,
"description": "One column: name and SQL type.",
"properties": {
"name": {
"description": "Column name.",
"type": "string"
},
"type": {
"description": "Column SQL type (DuckDB type).",
"type": "string"
}
},
"required": [
"name",
"type"
],
"type": "object"
},
"type": "array"
},
"name": {
"description": "Table name to reference in SQL.",
"type": "string"
},
"row_count": {
"description": "Number of rows in the table.",
"type": "number"
}
},
"required": [
"name",
"row_count",
"columns"
],
"type": "object"
},
"type": "array"
}
},
"type": "object"
}
},
{
"description": "Run a read-only SQL SELECT against a canvas table staged by gnomad_list_gene_variants (table gene_variants) or gnomad_search_clinvar (table clinvar_variants) and return one page of the result. Use the canvas_id and table_name those tools returned to rank by allele frequency, group by consequence class, count loss-of-function variants, or filter the full set the inline preview only sampled. A page holds up to limit rows (default 100, max 500) and ends early once its rows reach 10,000 characters of JSON; continue from next_offset until it is null. Each page re-runs the SQL, so stable paging needs an ORDER BY over a unique key (such as variant_id) and an unchanged table. Paging reaches the server row cap: above it total is null and later rows are reachable only by filtering or aggregating in SQL. SELECT statements only — writes, DDL, and file/HTTP table functions are rejected by the canvas gate. Call gnomad_dataframe_describe first to discover staged table and column names.",
"inputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"properties": {
"canvas_id": {
"description": "Canvas ID returned by gnomad_list_gene_variants or gnomad_search_clinvar.",
"pattern": "^[A-Za-z0-9_-]{10}$",
"type": "string"
},
"limit": {
"default": 100,
"description": "Maximum rows on the page (1–500). A page also ends before its rows pass 10,000 characters of JSON.",
"maximum": 500,
"minimum": 1,
"type": "integer"
},
"offset": {
"default": 0,
"description": "Row offset of the page to return. Start at 0, then pass next_offset from the previous page.",
"maximum": 9007199254740991,
"minimum": 0,
"type": "integer"
},
"sql": {
"description": "Read-only SQL SELECT. Reference tables by the names the staging tool returned (e.g. gene_variants). Add an ORDER BY over a unique key when paging.",
"minLength": 1,
"type": "string"
}
},
"required": [
"canvas_id",
"sql"
],
"type": "object"
},
"name": "gnomad_dataframe_query",
"outputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"rows",
"columns",
"offset",
"returned",
"total",
"truncated",
"next_offset"
]
},
{
"required": [
"error"
]
}
],
"properties": {
"columns": {
"description": "Column names in the result, in order.",
"items": {
"type": "string"
},
"type": "array"
},
"error": {
"additionalProperties": {},
"description": "Present when the call failed. Absent on success.",
"properties": {
"code": {
"description": "JSON-RPC error code for this failure.",
"maximum": 9007199254740991,
"minimum": -9007199254740991,
"type": "integer"
},
"data": {
"additionalProperties": {},
"properties": {
"reason": {
"description": "Machine-readable failure mode. Declared by this tool: `canvas_disabled`: DataCanvas is not enabled on this server instance. `row_too_large`: The first row of the requested page serializes to more than 10,000 characters of JSON, so no page can hold it. Other values are possible when a failure originates below the handler.",
"examples": [
"canvas_disabled",
"row_too_large"
],
"type": "string"
},
"recovery": {
"additionalProperties": {},
"description": "Actionable next step for the caller.",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"type": "object"
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"type": "object"
},
"message": {
"description": "Human-readable description of what went wrong.",
"type": "string"
}
},
"required": [
"code",
"message"
],
"type": "object"
},
"next_offset": {
"description": "offset for the next page; null when no page follows (end of the result, or the row cap reached).",
"type": [
"number",
"null"
]
},
"offset": {
"description": "Row offset this page starts at.",
"type": "number"
},
"returned": {
"description": "Rows on this page — fewer than limit when the 10,000-character row budget or the end of the result ends it early.",
"type": "number"
},
"rows": {
"description": "This page of result rows, in result order.",
"items": {
"additionalProperties": {},
"description": "One result row — dynamic columns per the SQL projection.",
"properties": {},
"type": "object"
},
"type": "array"
},
"total": {
"description": "Rows the SQL produced; null when the result exceeds the server row cap, whose later rows paging cannot reach.",
"type": [
"number",
"null"
]
},
"truncated": {
"description": "True when result rows exist after this page, including rows past the row cap that next_offset cannot reach.",
"type": "boolean"
}
},
"type": "object"
}
},
{
"description": "Fetch gnomAD sequencing-coverage summary across a gene, transcript, or region — mean and median read depth, plus the mean fraction of samples covered at each depth threshold (1× through 100×), separated by exome and genome track. Use this to disambiguate a true absent variant from an uncallable position: a variant missing from a well-covered region is informative, while one missing from a poorly-covered region is not. Supply exactly one of gene, transcript_id, or region. The optional coverage_source narrows to one track; by default both available tracks are returned. Echoes the effective dataset and build.\nData source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/",
"inputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"properties": {
"coverage_source": {
"description": "Restrict to one coverage track. Omit to return every available track.",
"enum": [
"exome",
"genome"
],
"type": "string"
},
"dataset": {
"description": "gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.",
"enum": [
"gnomad_r4",
"gnomad_r3",
"gnomad_r2_1",
"exac"
],
"type": "string"
},
"gene": {
"anyOf": [
{
"description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene.",
"minLength": 2,
"type": "string"
},
{
"description": "Blank — the gene is treated as omitted.",
"maxLength": 0,
"type": "string"
}
],
"description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted."
},
"reference_genome": {
"description": "Reference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.",
"enum": [
"GRCh38",
"GRCh37"
],
"type": "string"
},
"region": {
"anyOf": [
{
"const": "",
"type": "string"
},
{
"description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852) on chromosome 1–22, X, or Y, optional chr prefix.",
"pattern": "^(?:chr)?[0-9A-Z]+-\\d+-\\d+$",
"type": "string"
}
],
"description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852): chromosome 1–22, X, or Y with an optional chr prefix (mitochondrial regions are not served) and a span (stop − start) under 2,500,000 bp. Mutually exclusive with gene and transcript_id."
},
"transcript_id": {
"description": "Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted.",
"type": "string"
}
},
"type": "object"
},
"name": "gnomad_get_coverage",
"outputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"target",
"target_kind",
"summaries",
"dataset",
"reference_genome"
]
},
{
"required": [
"error"
]
}
],
"properties": {
"dataset": {
"description": "Effective gnomAD dataset.",
"type": "string"
},
"error": {
"additionalProperties": {},
"description": "Present when the call failed. Absent on success.",
"properties": {
"code": {
"description": "JSON-RPC error code for this failure.",
"maximum": 9007199254740991,
"minimum": -9007199254740991,
"type": "integer"
},
"data": {
"additionalProperties": {},
"properties": {
"reason": {
"description": "Machine-readable failure mode. Declared by this tool: `invalid_target`: Not exactly one of gene, transcript_id, or region was supplied. `incoherent_build`: reference_genome was supplied but does not match the dataset. `invalid_region`: The region names a chromosome outside 1–22, X, Y, or breaks the coordinate bounds. `region_too_large`: The region spans 2,500,000 bp or more, beyond what gnomAD summarizes at once. `mitochondrial_unsupported`: The gene, transcript, or region is on the mitochondrial chromosome (M or MT). `graphql_error`: gnomAD rejected the coverage query with a GraphQL error. `upstream_unavailable`: gnomAD stayed unavailable or throttled through every retry. `upstream_timeout`: Every attempt to reach gnomAD timed out. `upstream_access`: gnomAD refused the request (access denied). `invalid_upstream_response`: gnomAD kept answering with a response that failed validation. Other values are possible when a failure originates below the handler.",
"examples": [
"invalid_target",
"incoherent_build",
"invalid_region",
"region_too_large",
"mitochondrial_unsupported",
"graphql_error",
"upstream_unavailable",
"upstream_timeout",
"upstream_access",
"invalid_upstream_response"
],
"type": "string"
},
"recovery": {
"additionalProperties": {},
"description": "Actionable next step for the caller.",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"type": "object"
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"type": "object"
},
"message": {
"description": "Human-readable description of what went wrong.",
"type": "string"
}
},
"required": [
"code",
"message"
],
"type": "object"
},
"notice": {
"description": "Guidance when no coverage data is available for the target.",
"type": "string"
},
"reference_genome": {
"description": "Effective reference build.",
"type": "string"
},
"summaries": {
"description": "Per-track coverage summaries (exome and/or genome).",
"items": {
"additionalProperties": false,
"description": "Aggregate coverage for one callset track over the target.",
"properties": {
"fraction_over_1": {
"description": "Mean fraction of samples covered at ≥1×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_10": {
"description": "Mean fraction of samples covered at ≥10×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_100": {
"description": "Mean fraction of samples covered at ≥100×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_15": {
"description": "Mean fraction of samples covered at ≥15×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_20": {
"description": "Mean fraction of samples covered at ≥20×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_25": {
"description": "Mean fraction of samples covered at ≥25×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_30": {
"description": "Mean fraction of samples covered at ≥30×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_5": {
"description": "Mean fraction of samples covered at ≥5×; null when no data.",
"type": [
"number",
"null"
]
},
"fraction_over_50": {
"description": "Mean fraction of samples covered at ≥50×; null when no data.",
"type": [
"number",
"null"
]
},
"mean_depth": {
"description": "Mean read depth averaged across positions; null when no data.",
"type": [
"number",
"null"
]
},
"median_depth": {
"description": "Median read depth across positions; null when no data.",
"type": [
"number",
"null"
]
},
"positions": {
"description": "Number of base positions summarized across the target.",
"type": "number"
},
"source": {
"description": "Which gnomAD coverage track this summary covers.",
"enum": [
"exome",
"genome"
],
"type": "string"
}
},
"required": [
"source",
"positions",
"mean_depth",
"median_depth",
"fraction_over_1",
"fraction_over_5",
"fraction_over_10",
"fraction_over_15",
"fraction_over_20",
"fraction_over_25",
"fraction_over_30",
"fraction_over_50",
"fraction_over_100"
],
"type": "object"
},
"type": "array"
},
"target": {
"description": "The resolved target (gene symbol/ID, transcript ID, or region) the coverage describes.",
"type": "string"
},
"target_kind": {
"description": "Which target type was queried.",
"enum": [
"gene",
"transcript",
"region"
],
"type": "string"
}
},
"type": "object"
}
},
{
"description": "Fetch gnomAD loss-of-function constraint for a gene — pLI (probability of LoF intolerance; >0.9 intolerant), LOEUF (oe_lof_upper, the headline metric) plus its lower bound, observed/expected ratios for LoF, missense, and synonymous variation, and the three Z-scores. This is the orthogonal axis to allele frequency: a loss-of-function variant matters far more in a gene intolerant to being broken. Accepts an HGNC symbol (PCSK9) or an Ensembl gene ID (ENSG00000169174). constraint_release names the release the metrics come from: gnomAD v4.1.2 for gnomad_r4 and gnomad_r3 (gnomAD publishes no v3 constraint), gnomAD v2.1.1 for gnomad_r2_1, and ExAC r0.3 for exac. gnomAD recommends LOEUF < 0.45 to call a gene LoF-intolerant on v4.1.2 and LOEUF < 0.35 on v2.1.1. ExAC r0.3 publishes only pLI, the Z-scores, and observed/expected counts, so on exac the ratios and LOEUF are null, constraint_flags is empty, and pLI is the intolerance measure. Many genes have null constraint (sparse upstream) — null fields are reported as such, never fabricated. Echoes the effective dataset and reference build.\nData source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/",
"inputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"properties": {
"dataset": {
"description": "gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.",
"enum": [
"gnomad_r4",
"gnomad_r3",
"gnomad_r2_1",
"exac"
],
"type": "string"
},
"gene": {
"description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene.",
"minLength": 2,
"type": "string"
},
"reference_genome": {
"description": "Reference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.",
"enum": [
"GRCh38",
"GRCh37"
],
"type": "string"
}
},
"required": [
"gene"
],
"type": "object"
},
"name": "gnomad_get_gene_constraint",
"outputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"gene_id",
"symbol",
"dataset",
"reference_genome",
"constraint_release",
"pli",
"oe_lof",
"oe_lof_lower",
"oe_lof_upper",
"oe_mis",
"oe_syn",
"lof_z",
"mis_z",
"syn_z",
"obs_lof",
"exp_lof",
"obs_mis",
"exp_mis",
"obs_syn",
"exp_syn",
"constraint_flags"
]
},
{
"required": [
"error"
]
}
],
"properties": {
"constraint_flags": {
"description": "Caveat flags gnomAD attaches to the gene’s constraint (e.g. no_exp_lof, mis_too_many, syn_outlier); empty when none, and always empty on exac, where ExAC publishes no flags.",
"items": {
"type": "string"
},
"type": "array"
},
"constraint_release": {
"description": "Constraint release the metrics come from: gnomAD v4.1.2 for gnomad_r4 and gnomad_r3 (gnomAD publishes no v3 constraint, so gnomad_r3 serves the GRCh38 table), gnomAD v2.1.1 for gnomad_r2_1, ExAC r0.3 for exac.",
"type": "string"
},
"dataset": {
"description": "Effective gnomAD dataset.",
"type": "string"
},
"error": {
"additionalProperties": {},
"description": "Present when the call failed. Absent on success.",
"properties": {
"code": {
"description": "JSON-RPC error code for this failure.",
"maximum": 9007199254740991,
"minimum": -9007199254740991,
"type": "integer"
},
"data": {
"additionalProperties": {},
"properties": {
"reason": {
"description": "Machine-readable failure mode. Declared by this tool: `gene_not_found`: No gene matched the symbol or Ensembl ID in this build. `incoherent_build`: reference_genome was supplied but does not match the dataset. `invalid_constraint_data`: gnomAD returned constraint metrics outside their valid ranges, such as a pLI above 1. `graphql_error`: gnomAD rejected the constraint query with a GraphQL error. `upstream_unavailable`: gnomAD stayed unavailable or throttled through every retry. `upstream_timeout`: Every attempt to reach gnomAD timed out. `upstream_access`: gnomAD refused the request (access denied). `invalid_upstream_response`: gnomAD kept answering with a response that failed validation. Other values are possible when a failure originates below the handler.",
"examples": [
"gene_not_found",
"incoherent_build",
"invalid_constraint_data",
"graphql_error",
"upstream_unavailable",
"upstream_timeout",
"upstream_access",
"invalid_upstream_response"
],
"type": "string"
},
"recovery": {
"additionalProperties": {},
"description": "Actionable next step for the caller.",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"type": "object"
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"type": "object"
},
"message": {
"description": "Human-readable description of what went wrong.",
"type": "string"
}
},
"required": [
"code",
"message"
],
"type": "object"
},
"exp_lof": {
"anyOf": [
{
"minimum": 0,
"type": "number"
},
{
"type": "null"
}
],
"description": "Non-negative expected LoF variant count. Null when unavailable."
},
"exp_mis": {
"anyOf": [
{
"minimum": 0,
"type": "number"
},
{
"type": "null"
}
],
"description": "Non-negative expected missense count. Null when unavailable."
},
"exp_syn": {
"anyOf": [
{
"minimum": 0,
"type": "number"
},
{
"type": "null"
}
],
"description": "Non-negative expected synonymous count. Null when unavailable."
},
"gene_id": {
"description": "Ensembl gene ID resolved for the gene.",
"type": "string"
},
"lof_z": {
"description": "LoF constraint Z-score. Null when unavailable.",
"type": [
"number",
"null"
]
},
"mis_z": {
"description": "Missense constraint Z-score. Null when unavailable.",
"type": [
"number",
"null"
]
},
"obs_lof": {
"anyOf": [
{
"minimum": 0,
"type": "number"
},
{
"type": "null"
}
],
"description": "Non-negative observed LoF variant count. Null when unavailable."
},
"obs_mis": {
"anyOf": [
{
"minimum": 0,
"type": "number"
},
{
"type": "null"
}
],
"description": "Non-negative observed missense count. Null when unavailable."
},
"obs_syn": {
"anyOf": [
{
"minimum": 0,
"type": "number"
},
{
"type": "null"
}
],
"description": "Non-negative observed synonymous count. Null when unavailable."
},
"oe_lof": {
"anyOf": [
{
"minimum": 0,
"type": "number"
},
{
"type": "null"
}
],
"description": "Non-negative observed/expected LoF ratio. Null when unavailable."
},
"oe_lof_lower": {
"anyOf": [
{
"minimum": 0,
"type": "number"
},
{
"type": "null"
}
],
"description": "LOEUF confidence-interval lower bound. Null when unavailable."
},
"oe_lof_upper": {
"anyOf": [
{
"minimum": 0,
"type": "number"
},
{
"type": "null"
}
],
"description": "LOEUF (oe_lof_upper) — the headline intolerance metric; gnomAD recommends < 0.45 on v4.1.2 and < 0.35 on v2.1.1 to call a gene LoF-intolerant. Null when unavailable, and always null on exac."
},
"oe_mis": {
"anyOf": [
{
"minimum": 0,
"type": "number"
},
{
"type": "null"
}
],
"description": "Observed/expected missense ratio. Null when unavailable."
},
"oe_syn": {
"anyOf": [
{
"minimum": 0,
"type": "number"
},
{
"type": "null"
}
],
"description": "Observed/expected synonymous ratio. Null when unavailable."
},
"pli": {
"anyOf": [
{
"maximum": 1,
"minimum": 0,
"type": "number"
},
{
"type": "null"
}
],
"description": "pLI — probability of LoF intolerance; >0.9 intolerant. Null when unavailable."
},
"reference_genome": {
"description": "Effective reference build.",
"type": "string"
},
"symbol": {
"description": "HGNC gene symbol.",
"type": "string"
},
"syn_z": {
"description": "Synonymous constraint Z-score. Null when unavailable.",
"type": [
"number",
"null"
]
}
},
"type": "object"
}
},
{
"description": "Fetch the full gnomAD population record for one or more variants — allele count/number/frequency overall and broken down per genetic-ancestry group, homozygote and hemizygote counts, quality flags, transcript consequence, in-silico predictor scores, and joined ClinVar clinical significance. The \"how common, is it benign\" answer in one call. Accepts a batch of up to 25 IDs (chrom-pos-ref-alt or rsID) with per-item partial success: a malformed or absent ID lands in failed[] — with its reason and a recovery hint — without failing the others. An empty found[] for a well-formed ID means the variant is not in the chosen dataset — pair with gnomad_get_coverage to confirm the position is callable before concluding true absence.\nData source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/",
"inputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"properties": {
"dataset": {
"description": "gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.",
"enum": [
"gnomad_r4",
"gnomad_r3",
"gnomad_r2_1",
"exac"
],
"type": "string"
},
"reference_genome": {
"description": "Reference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.",
"enum": [
"GRCh38",
"GRCh37"
],
"type": "string"
},
"variants": {
"description": "1–25 variant IDs (chrom-pos-ref-alt or rsID) to look up in one batched call.",
"items": {
"description": "Variant ID — chrom-pos-ref-alt (1-based, e.g. 1-55051215-G-GA) on chromosome 1–22, X, or Y with an optional chr prefix, or an rsID (rs11591147). Mitochondrial IDs (M, MT, chrM) are not served. Obtain a variantId from ensembl_predict_variant or a VCF. Malformed IDs are reported per-item in failed[], not rejected wholesale.",
"minLength": 1,
"type": "string"
},
"maxItems": 25,
"minItems": 1,
"type": "array"
}
},
"required": [
"variants"
],
"type": "object"
},
"name": "gnomad_get_variant",
"outputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"found",
"failed",
"dataset",
"reference_genome"
]
},
{
"required": [
"error"
]
}
],
"properties": {
"dataset": {
"description": "Effective gnomAD dataset used for the batch.",
"type": "string"
},
"error": {
"additionalProperties": {},
"description": "Present when the call failed. Absent on success.",
"properties": {
"code": {
"description": "JSON-RPC error code for this failure.",
"maximum": 9007199254740991,
"minimum": -9007199254740991,
"type": "integer"
},
"data": {
"additionalProperties": {},
"properties": {
"reason": {
"description": "Machine-readable failure mode. Declared by this tool: `incoherent_build`: reference_genome was supplied but does not match the dataset. `invalid_variant_id`: A variant ID is outside the chrom-pos-ref-alt or rsID grammar; reported per item in failed[]. `variant_not_found`: A well-formed ID is absent from the requested dataset; reported per item in failed[]. `mitochondrial_unsupported`: A variant ID names the mitochondrial chromosome (M, MT, or chrM); reported per item in failed[]. `ambiguous_rsid`: An rsID maps to more than one variant in the dataset; reported per item in failed[]. `graphql_error`: gnomAD rejected the lookup for one ID with a GraphQL error; reported per item in failed[]. `upstream_build_mismatch`: gnomAD answered one ID with a variant on a different reference build; reported per item in failed[]. `upstream_unavailable`: gnomAD stayed unavailable or throttled through every retry for one ID; reported per item in failed[]. `upstream_timeout`: Every attempt to reach gnomAD for one ID timed out; reported per item in failed[]. `upstream_access`: gnomAD refused the request for one ID (access denied); reported per item in failed[]. `invalid_upstream_response`: gnomAD kept answering one ID with a response that failed validation; reported per item in failed[]. Other values are possible when a failure originates below the handler.",
"examples": [
"incoherent_build",
"invalid_variant_id",
"variant_not_found",
"mitochondrial_unsupported",
"ambiguous_rsid",
"graphql_error",
"upstream_build_mismatch",
"upstream_unavailable",
"upstream_timeout",
"upstream_access",
"invalid_upstream_response"
],
"type": "string"
},
"recovery": {
"additionalProperties": {},
"description": "Actionable next step for the caller.",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"type": "object"
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"type": "object"
},
"message": {
"description": "Human-readable description of what went wrong.",
"type": "string"
}
},
"required": [
"code",
"message"
],
"type": "object"
},
"failed": {
"description": "Per-item failures, in input order: malformed IDs, variants absent from the dataset, or upstream errors — each with its reason and recovery hint.",
"items": {
"additionalProperties": false,
"description": "One failed input ID, why it failed, and what to do next.",
"properties": {
"candidates": {
"description": "Concrete variant IDs to retry when an rsID is ambiguous.",
"items": {
"type": "string"
},
"type": "array"
},
"error": {
"description": "What went wrong for this ID.",
"type": "string"
},
"reason": {
"description": "Why this ID failed — a reason declared in this tool's error contract. Branch on it rather than on the message.",
"enum": [
"invalid_variant_id",
"variant_not_found",
"mitochondrial_unsupported",
"ambiguous_rsid",
"graphql_error",
"upstream_build_mismatch",
"upstream_unavailable",
"upstream_timeout",
"upstream_access",
"invalid_upstream_response"
],
"type": "string"
},
"recovery": {
"description": "The next step for this ID — the recovery hint declared for its reason.",
"type": "string"
},
"variant": {
"description": "The input ID that failed to resolve.",
"type": "string"
}
},
"required": [
"variant",
"error",
"reason",
"recovery"
],
"type": "object"
},
"type": "array"
},
"found": {
"description": "Variants resolved to a population record.",
"items": {
"additionalProperties": false,
"description": "Full population record for one variant.",
"properties": {
"ac": {
"description": "Overall allele count across carried callset(s).",
"type": "number"
},
"af": {
"description": "Overall allele frequency; null when an is 0.",
"type": [
"number",
"null"
]
},
"an": {
"description": "Overall allele number across carried callset(s).",
"type": "number"
},
"clinvar": {
"anyOf": [
{
"additionalProperties": false,
"description": "Joined ClinVar significance from gnomAD. Null when the variant has no ClinVar entry.",
"properties": {
"clinical_significance": {
"description": "ClinVar clinical significance (e.g. Pathogenic, Likely benign); null when no entry.",
"type": [
"string",
"null"
]
},
"clinvar_variation_id": {
"description": "ClinVar VariationID.",
"type": [
"string",
"null"
]
},
"gold_stars": {
"description": "ClinVar 0–4 star review rating.",
"type": [
"number",
"null"
]
},
"review_status": {
"description": "ClinVar review status text.",
"type": [
"string",
"null"
]
}
},
"required": [
"clinical_significance",
"review_status",
"gold_stars",
"clinvar_variation_id"
],
"type": "object"
},
{
"type": "null"
}
],
"description": "ClinVar annotation, or null when no entry exists."
},
"clinvar_unavailable": {
"description": "True when the optional ClinVar resolver failed; false when no entry exists.",
"type": "boolean"
},
"consequence": {
"description": "Worst/transcript VEP consequence term; null when none.",
"type": [
"string",
"null"
]
},
"dataset": {
"description": "Effective gnomAD dataset.",
"type": "string"
},
"flags": {
"description": "Quality flags (e.g. lcr, segdup, lc_lof).",
"items": {
"type": "string"
},
"type": "array"
},
"gene_symbol": {
"description": "Gene symbol for the reported consequence; null when none.",
"type": [
"string",
"null"
]
},
"hemizygote_count": {
"description": "Overall hemizygote count (X/Y only); null otherwise.",
"type": [
"number",
"null"
]
},
"homozygote_count": {
"description": "Overall homozygote count.",
"type": "number"
},
"in_silico": {
"description": "In-silico predictor scores present for this variant.",
"items": {
"additionalProperties": false,
"description": "One in-silico predictor score.",
"properties": {
"annotation": {
"description": "Text gnomAD attaches to the score — on gnomad_r3, the SpliceAI event (e.g. acceptor_gain, no_consequence). Holds the raw text when value is null for lack of a number; null for a plain score.",
"type": [
"string",
"null"
]
},
"id": {
"description": "Predictor name. Ids vary by dataset — gnomad_r4: cadd, revel_max, spliceai_ds_max, pangolin_largest_ds, phylop, sift_max, polyphen_max; gnomad_r3: cadd, revel, splice_ai, primate_ai; gnomad_r2_1 and exac carry none.",
"type": "string"
},
"value": {
"description": "Predictor score; null when not provided for this variant, or when gnomAD gave text with no number (the text is then in annotation).",
"type": [
"number",
"null"
]
}
},
"required": [
"id",
"value",
"annotation"
],
"type": "object"
},
"type": "array"
},
"populations": {
"description": "Per-ancestry frequency vector — never collapsed to a single global AF.",
"items": {
"additionalProperties": false,
"description": "One genetic-ancestry group AC/AN/AF vector.",
"properties": {
"ac": {
"description": "Allele count in this group.",
"type": "number"
},
"af": {
"description": "Allele frequency (ac/an); null when an is 0.",
"type": [
"number",
"null"
]
},
"an": {
"description": "Allele number (called chromosomes) in this group.",
"type": "number"
},
"hemizygote_count": {
"description": "Hemizygote count (X/Y only); null otherwise.",
"type": [
"number",
"null"
]
},
"homozygote_count": {
"description": "Homozygote count in this group.",
"type": "number"
},
"id": {
"description": "Genetic-ancestry group: afr, amr, asj, eas, fin, mid, nfe, sas, remaining, or ami (genomes only).",
"type": "string"
},
"source": {
"description": "Which gnomAD callset this group vector came from.",
"enum": [
"exome",
"genome"
],
"type": "string"
}
},
"required": [
"id",
"source",
"ac",
"an",
"af",
"homozygote_count",
"hemizygote_count"
],
"type": "object"
},
"type": "array"
},
"reference_genome": {
"description": "Reference build the record is on (GRCh38 or GRCh37).",
"type": "string"
},
"rsids": {
"description": "dbSNP rsIDs for this variant.",
"items": {
"type": "string"
},
"type": "array"
},
"source": {
"description": "Which gnomAD callset(s) carry this variant.",
"items": {
"enum": [
"exome",
"genome"
],
"type": "string"
},
"type": "array"
},
"transcript_id": {
"description": "Transcript the consequence is on; null when none.",
"type": [
"string",
"null"
]
},
"variant_id": {
"description": "Resolved chrom-pos-ref-alt variant ID.",
"type": "string"
}
},
"required": [
"variant_id",
"rsids",
"reference_genome",
"dataset",
"ac",
"an",
"af",
"homozygote_count",
"hemizygote_count",
"populations",
"source",
"flags",
"consequence",
"transcript_id",
"gene_symbol",
"in_silico",
"clinvar",
"clinvar_unavailable"
],
"type": "object"
},
"type": "array"
},
"notice": {
"description": "Non-fatal notice when optional ClinVar annotation was unavailable.",
"type": "string"
},
"reference_genome": {
"description": "Effective reference build used for the batch.",
"type": "string"
}
},
"type": "object"
}
},
{
"description": "List every gnomAD variant in a gene, transcript, or region with allele frequencies and predicted consequences, optionally filtered to one consequence class (lof, missense, synonymous, other) and/or a maximum allele frequency. A result too large to inline is staged on a DataCanvas table named gene_variants, returned as canvas_id and table_name beside an inline preview — call gnomad_dataframe_describe for its columns, then gnomad_dataframe_query to rank by AF, count by consequence, or group across every row rather than the preview. A result that fits inline stages no table unless canvas_id is supplied. When the canvas is disabled (CANVAS_PROVIDER_TYPE != duckdb) the tool returns a capped inline preview and the SQL path is unavailable. Supply exactly one of gene, transcript_id, or region. Echoes the effective dataset and build.\nData source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/",
"inputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"properties": {
"canvas_id": {
"description": "Optional canvas ID from a prior call, to reuse the same canvas. When supplied, this call always writes its result to the gene_variants table on that canvas, replacing (not appending to) the previous one — even when the result fits inline; a result with no variants removes the table. Omit to stage on a fresh canvas only when the result is too large to inline.",
"pattern": "^[A-Za-z0-9_-]{10}$",
"type": "string"
},
"consequence_class": {
"description": "Keep only variants in this consequence class. Omit to return all classes.",
"enum": [
"lof",
"missense",
"synonymous",
"other"
],
"type": "string"
},
"dataset": {
"description": "gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.",
"enum": [
"gnomad_r4",
"gnomad_r3",
"gnomad_r2_1",
"exac"
],
"type": "string"
},
"gene": {
"anyOf": [
{
"description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene.",
"minLength": 2,
"type": "string"
},
{
"description": "Blank — the gene is treated as omitted.",
"maxLength": 0,
"type": "string"
}
],
"description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted."
},
"max_af": {
"description": "Keep only variants with allele frequency ≤ this value (0–1). Variants with null AF are always kept.",
"maximum": 1,
"minimum": 0,
"type": "number"
},
"reference_genome": {
"description": "Reference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.",
"enum": [
"GRCh38",
"GRCh37"
],
"type": "string"
},
"region": {
"anyOf": [
{
"const": "",
"type": "string"
},
{
"description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 13-32315474-32400266) on chromosome 1–22, X, or Y, optional chr prefix.",
"pattern": "^(?:chr)?[0-9A-Z]+-\\d+-\\d+$",
"type": "string"
}
],
"description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 13-32315474-32400266): chromosome 1–22, X, or Y with an optional chr prefix (mitochondrial regions are not served), a span (stop − start) under 2,500,000 bp, and at most ~30,000 variants. Mutually exclusive with gene and transcript_id."
},
"transcript_id": {
"description": "Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted.",
"type": "string"
}
},
"type": "object"
},
"name": "gnomad_list_gene_variants",
"outputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"preview",
"canvas_id",
"table_name",
"spilled",
"total",
"dataset",
"reference_genome"
]
},
{
"required": [
"error"
]
}
],
"properties": {
"canvas_id": {
"description": "Canvas holding table_name (or the canvas_id you supplied) — pass it to gnomad_dataframe_describe, then gnomad_dataframe_query. Empty when this call used no canvas: the result fit inline and no canvas_id was supplied, or the canvas is disabled.",
"type": "string"
},
"dataset": {
"description": "Effective gnomAD dataset.",
"type": "string"
},
"error": {
"additionalProperties": {},
"description": "Present when the call failed. Absent on success.",
"properties": {
"code": {
"description": "JSON-RPC error code for this failure.",
"maximum": 9007199254740991,
"minimum": -9007199254740991,
"type": "integer"
},
"data": {
"additionalProperties": {},
"properties": {
"reason": {
"description": "Machine-readable failure mode. Declared by this tool: `invalid_target`: Not exactly one of gene, transcript_id, or region was supplied. `incoherent_build`: reference_genome was supplied but does not match the dataset. `invalid_region`: The region names a chromosome outside 1–22, X, Y, or breaks the coordinate bounds. `region_too_large`: The region spans 2,500,000 bp or more, or holds more variants (~30,000) than gnomAD lists at once. `mitochondrial_unsupported`: The gene, transcript, or region is on the mitochondrial chromosome (M or MT). `graphql_error`: gnomAD rejected the variant-list query with a GraphQL error. `upstream_unavailable`: gnomAD stayed unavailable or throttled through every retry. `upstream_timeout`: Every attempt to reach gnomAD timed out. `upstream_access`: gnomAD refused the request (access denied). `invalid_upstream_response`: gnomAD kept answering with a response that failed validation. Other values are possible when a failure originates below the handler.",
"examples": [
"invalid_target",
"incoherent_build",
"invalid_region",
"region_too_large",
"mitochondrial_unsupported",
"graphql_error",
"upstream_unavailable",
"upstream_timeout",
"upstream_access",
"invalid_upstream_response"
],
"type": "string"
},
"recovery": {
"additionalProperties": {},
"description": "Actionable next step for the caller.",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"type": "object"
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"type": "object"
},
"message": {
"description": "Human-readable description of what went wrong.",
"type": "string"
}
},
"required": [
"code",
"message"
],
"type": "object"
},
"notice": {
"description": "Guidance when no variants matched, when the canvas is disabled and the preview is capped, and — when a table was staged — its name with the next steps: gnomad_dataframe_describe, then gnomad_dataframe_query.",
"type": "string"
},
"preview": {
"description": "Inline preview rows — the immediate answer; every matching variant unless spilled.",
"items": {
"additionalProperties": false,
"description": "One gene-variant row — also the canvas table column set.",
"properties": {
"ac": {
"description": "Allele count (joint across carried callsets).",
"type": "number"
},
"af": {
"description": "Allele frequency computed from joint allele counts; null when uncomputable.",
"type": [
"number",
"null"
]
},
"an": {
"description": "Allele number (joint sum across carried callsets).",
"type": "number"
},
"consequence": {
"description": "VEP consequence term; null when none.",
"type": [
"string",
"null"
]
},
"consequence_class": {
"description": "Bucketed consequence class.",
"enum": [
"lof",
"missense",
"synonymous",
"other"
],
"type": "string"
},
"flags": {
"description": "Quality flags, pipe-joined (empty when none).",
"type": "string"
},
"homozygote_count": {
"description": "Homozygote count (joint across callsets).",
"type": "number"
},
"source": {
"description": "Carried callset(s), pipe-joined (e.g. exome|genome).",
"type": "string"
},
"variant_id": {
"description": "chrom-pos-ref-alt variant ID.",
"type": "string"
}
},
"required": [
"variant_id",
"af",
"ac",
"an",
"consequence",
"consequence_class",
"homozygote_count",
"source",
"flags"
],
"type": "object"
},
"type": "array"
},
"reference_genome": {
"description": "Effective reference build.",
"type": "string"
},
"spilled": {
"description": "True when the result exceeded the inline preview budget, so the preview holds only the first rows and table_name holds them all.",
"type": "boolean"
},
"table_name": {
"description": "Canvas table this call staged (gene_variants), holding every matching variant — inspect it with gnomad_dataframe_describe, then query it with gnomad_dataframe_query. Empty when this call staged no table.",
"type": "string"
},
"total": {
"description": "Total matching variants, including any beyond the preview.",
"type": "number"
}
},
"type": "object"
}
},
{
"description": "Search ClinVar (NCBI E-utilities) for a gene and return its classified variants — clinical significance, review status with a 0–4 star rating, associated conditions, molecular consequences, submission counts, and gnomAD-compatible identifiers (canonical SPDI, rsIDs, GRCh38 variant ID for gnomad_get_variant) — turning the variant-level significance gnomAD joins into a gene-panel curation view. Optionally filter by clinical_significance (e.g. pathogenic) and a minimum star rating. Each call returns one window of up to 500 ClinVar records: total_found is the ClinVar candidate count for the search terms, taken before the significance and star filters narrow each window, and next_offset continues through the rest via offset. A window too large to inline is staged on a DataCanvas table named clinvar_variants, returned as canvas_id and table_name beside an inline preview — call gnomad_dataframe_describe for its columns, then gnomad_dataframe_query to rank or count across the window. A window that fits inline stages no table unless canvas_id is supplied. Keyless, but honors NCBI_API_KEY for a higher rate limit. When the canvas is disabled the tool returns a capped inline preview. Credit: ClinVar, NCBI.",
"inputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"properties": {
"canvas_id": {
"description": "Optional canvas ID from a prior call, to reuse the same canvas. When supplied, each search writes its window to the clinvar_variants table on that canvas, replacing (not appending to) the previous one — even when the window fits inline; a window with no rows removes the table. An Ensembl gene ID searches nothing and leaves the canvas as it was. Omit to stage on a fresh canvas only when the window is too large to inline.",
"pattern": "^[A-Za-z0-9_-]{10}$",
"type": "string"
},
"clinical_significance": {
"description": "Filter by ClinVar clinical significance term (e.g. pathogenic, likely_pathogenic, uncertain significance), matched as whole words; underscores read as spaces. Blank means no filter.",
"type": "string"
},
"gene": {
"description": "Gene HGNC symbol (e.g. PCSK9). ClinVar indexes HGNC symbols only — Ensembl gene IDs (ENSG…) are not resolved here, unlike the other gnomAD tools; resolve one to its symbol via ensembl_lookup_gene.",
"minLength": 2,
"type": "string"
},
"limit": {
"default": 500,
"description": "ClinVar records to fetch in this window (1–500). Counted before the clinical_significance and min_review_stars filters, so a window can return fewer rows.",
"maximum": 500,
"minimum": 1,
"type": "integer"
},
"min_review_stars": {
"description": "Keep only variants with at least this gold-star review rating (0–4).",
"maximum": 4,
"minimum": 0,
"type": "integer"
},
"offset": {
"default": 0,
"description": "Zero-based position of the first ClinVar record in this window. Pass next_offset from the previous call to continue.",
"maximum": 2147483647,
"minimum": 0,
"type": "integer"
}
},
"required": [
"gene"
],
"type": "object"
},
"name": "gnomad_search_clinvar",
"outputSchema": {
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"preview",
"canvas_id",
"table_name",
"spilled",
"total",
"total_found",
"truncated",
"next_offset",
"unavailable_ids"
]
},
{
"required": [
"error"
]
}
],
"properties": {
"canvas_id": {
"description": "Canvas holding table_name (or the canvas_id you supplied) — pass it to gnomad_dataframe_describe, then gnomad_dataframe_query. Empty when this call used no canvas: the window fit inline and no canvas_id was supplied, the gene was an Ensembl ID (nothing was searched), or the canvas is disabled.",
"type": "string"
},
"error": {
"additionalProperties": {},
"description": "Present when the call failed. Absent on success.",
"properties": {
"code": {
"description": "JSON-RPC error code for this failure.",
"maximum": 9007199254740991,
"minimum": -9007199254740991,
"type": "integer"
},
"data": {
"additionalProperties": {},
"properties": {
"reason": {
"description": "Machine-readable failure mode. Declared by this tool: `upstream_unavailable`: NCBI E-utilities is unreachable, failing, or rate-limiting after retries. `upstream_timeout`: Every attempt to reach NCBI E-utilities timed out. `upstream_access`: NCBI E-utilities refused the request (access denied). `invalid_upstream_response`: NCBI E-utilities kept answering with a response that failed validation. Other values are possible when a failure originates below the handler.",
"examples": [
"upstream_unavailable",
"upstream_timeout",
"upstream_access",
"invalid_upstream_response"
],
"type": "string"
},
"recovery": {
"additionalProperties": {},
"description": "Actionable next step for the caller.",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"type": "object"
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"type": "object"
},
"message": {
"description": "Human-readable description of what went wrong.",
"type": "string"
}
},
"required": [
"code",
"message"
],
"type": "object"
},
"next_offset": {
"description": "offset for the next window; null when this window reaches the end.",
"type": [
"number",
"null"
]
},
"notice": {
"description": "Guidance on completeness (the offset that continues the list, or an offset past the end), no-match results, a capped preview when the canvas is disabled, the staged table with its next steps (gnomad_dataframe_describe, then gnomad_dataframe_query), and which identifier to pass to gnomad_get_variant.",
"type": "string"
},
"preview": {
"description": "Inline preview rows — the immediate answer; the window's every row unless spilled.",
"items": {
"additionalProperties": false,
"description": "One ClinVar variant row — also the canvas table column set.",
"properties": {
"accession": {
"description": "ClinVar accession (e.g. VCV004855003).",
"type": "string"
},
"canonical_spdi": {
"description": "Canonical SPDI of the variant (GRCh38, e.g. NC_000001.11:55039973:G:T); null for multi-allele records, CNVs, and records without one.",
"type": [
"string",
"null"
]
},
"clinical_significance": {
"description": "Germline classification (e.g. Pathogenic); null when none.",
"type": [
"string",
"null"
]
},
"clinvar_variation_id": {
"description": "ClinVar VariationID (uid).",
"type": "string"
},
"conditions": {
"description": "Associated conditions/traits, semicolon-joined.",
"type": "string"
},
"gold_stars": {
"description": "0–4 star review rating derived from review status.",
"type": "number"
},
"grch38_variant_id": {
"description": "gnomAD variant ID (chrom-pos-ref-alt, GRCh38) for gnomad_get_variant with the GRCh38 datasets (gnomad_r4, gnomad_r3). Set for SNVs, MNVs, and delins; null for deletions, insertions, duplications, mitochondrial variants, and multi-allele records.",
"type": [
"string",
"null"
]
},
"last_evaluated": {
"description": "Date the classification was last evaluated; null when unknown.",
"type": [
"string",
"null"
]
},
"molecular_consequences": {
"description": "Molecular consequences, semicolon-joined.",
"type": "string"
},
"obj_type": {
"description": "Variant object type (e.g. single nucleotide variant).",
"type": "string"
},
"protein_change": {
"description": "Protein change(s), comma-joined as ClinVar reports them.",
"type": "string"
},
"review_status": {
"description": "ClinVar review-status text; null when none.",
"type": [
"string",
"null"
]
},
"rsids": {
"description": "dbSNP rsIDs (e.g. rs11591147), semicolon-joined; empty when none. One rsID can match several gnomAD variants, so prefer grch38_variant_id for gnomad_get_variant.",
"type": "string"
},
"submission_count": {
"description": "Number of submitted (SCV) records.",
"type": "number"
},
"title": {
"description": "Variant title (HGVS expression).",
"type": "string"
}
},
"required": [
"clinvar_variation_id",
"accession",
"title",
"obj_type",
"clinical_significance",
"review_status",
"gold_stars",
"last_evaluated",
"molecular_consequences",
"protein_change",
"conditions",
"submission_count",
"canonical_spdi",
"rsids",
"grch38_variant_id"
],
"type": "object"
},
"type": "array"
},
"spilled": {
"description": "True when this window's rows exceeded the inline preview budget, so the preview holds only the first rows and table_name holds them all.",
"type": "boolean"
},
"table_name": {
"description": "Canvas table this call staged (clinvar_variants), holding this window's rows — inspect it with gnomad_dataframe_describe, then query it with gnomad_dataframe_query. Empty when this call staged no table.",
"type": "string"
},
"total": {
"description": "Rows in this window that passed the filters, including any beyond the preview.",
"type": "number"
},
"total_found": {
"description": "ClinVar records matching the gene and filter terms across every window, counted before the post-fetch significance and star filters.",
"type": "number"
},
"truncated": {
"description": "True when ClinVar records remain past this window; continue with next_offset.",
"type": "boolean"
},
"unavailable_ids": {
"description": "VariationIDs in this window that ClinVar returned no summary for, so they have no row; empty when none.",
"items": {
"type": "string"
},
"type": "array"
}
},
"type": "object"
}
}
]
}Verify it yourself
curl -s https://api.teppi.xyz/v1/evidence/sha256:14222822b535bc33580aa4aee2cc0fc3757a2e423ebca48884fe527866eb2a43 | sha256sum