gnomad-genetics-mcp-server

{'type': 'object', '$schema': 'https://json-schema.org/draft/2020-12/schema', 'required': ['canvas_id'], 'properties': {'canvas_id': {'type': 'string', 'pattern': '^[A-Za-z0-9_-]{10}$', 'description': 'Canvas ID returned by a prior staging call (gnomad_list_gene_variants or gnomad_search_clinvar).'}}, 'additionalProperties': False}

{'type': 'object', 'anyOf': [{'not': {'required': ['error']}, 'required': ['tables']}, {'required': ['error']}], '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'error': {'type': 'object', 'required': ['code', 'message'], 'properties': {'code': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991, 'description': 'JSON-RPC error code for this failure.'}, 'data': {'type': 'object', 'properties': {'reason': {'type': 'string', 'examples': ['canvas_disabled'], '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.'}, 'recovery': {'type': 'object', 'required': ['hint'], 'properties': {'hint': {'type': 'string'}}, 'description': 'Actionable next step for the caller.', 'additionalProperties': {}}, 'retryable': {'type': 'boolean', 'description': 'Whether retrying may succeed.'}}, 'additionalProperties': {}}, 'message': {'type': 'string', 'description': 'Human-readable description of what went wrong.'}}, 'description': 'Present when the call failed. Absent on success.', 'additionalProperties': {}}, 'tables': {'type': 'array', 'items': {'type': 'object', 'required': ['name', 'row_count', 'columns'], 'properties': {'name': {'type': 'string', 'description': 'Table name to reference in SQL.'}, 'columns': {'type': 'array', 'items': {'type': 'object', 'required': ['name', 'type'], 'properties': {'name': {'type': 'string', 'description': 'Column name.'}, 'type': {'type': 'string', 'description': 'Column SQL type (DuckDB type).'}}, 'description': 'One column: name and SQL type.', 'additionalProperties': False}, 'description': 'Column schema, in order.'}, 'row_count': {'type': 'number', 'description': 'Number of rows in the table.'}}, 'description': 'One staged table: name, row count, and column schema.', 'additionalProperties': False}, 'description': 'Tables staged on the canvas.'}}, 'additionalProperties': False}

{'type': 'object', '$schema': 'https://json-schema.org/draft/2020-12/schema', 'required': ['canvas_id', 'sql'], 'properties': {'sql': {'type': 'string', 'minLength': 1, 'description': 'Read-only SQL SELECT. Reference tables by the names the staging tool returned (e.g. gene_variants). Add an ORDER BY over a unique key when paging.'}, 'limit': {'type': 'integer', 'default': 100, 'maximum': 500, 'minimum': 1, 'description': 'Maximum rows on the page (1â\x80\x93500). A page also ends before its rows pass 10,000 characters of JSON.'}, 'offset': {'type': 'integer', 'default': 0, 'maximum': 9007199254740991, 'minimum': 0, 'description': 'Row offset of the page to return. Start at 0, then pass next_offset from the previous page.'}, 'canvas_id': {'type': 'string', 'pattern': '^[A-Za-z0-9_-]{10}$', 'description': 'Canvas ID returned by gnomad_list_gene_variants or gnomad_search_clinvar.'}}, 'additionalProperties': False}

{'type': 'object', 'anyOf': [{'not': {'required': ['error']}, 'required': ['rows', 'columns', 'offset', 'returned', 'total', 'truncated', 'next_offset']}, {'required': ['error']}], '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'rows': {'type': 'array', 'items': {'type': 'object', 'properties': {}, 'description': 'One result row â\x80\x94 dynamic columns per the SQL projection.', 'additionalProperties': {}}, 'description': 'This page of result rows, in result order.'}, 'error': {'type': 'object', 'required': ['code', 'message'], 'properties': {'code': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991, 'description': 'JSON-RPC error code for this failure.'}, 'data': {'type': 'object', 'properties': {'reason': {'type': 'string', 'examples': ['canvas_disabled', 'row_too_large'], '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.'}, 'recovery': {'type': 'object', 'required': ['hint'], 'properties': {'hint': {'type': 'string'}}, 'description': 'Actionable next step for the caller.', 'additionalProperties': {}}, 'retryable': {'type': 'boolean', 'description': 'Whether retrying may succeed.'}}, 'additionalProperties': {}}, 'message': {'type': 'string', 'description': 'Human-readable description of what went wrong.'}}, 'description': 'Present when the call failed. Absent on success.', 'additionalProperties': {}}, 'total': {'type': ['number', 'null'], 'description': 'Rows the SQL produced; null when the result exceeds the server row cap, whose later rows paging cannot reach.'}, 'offset': {'type': 'number', 'description': 'Row offset this page starts at.'}, 'columns': {'type': 'array', 'items': {'type': 'string'}, 'description': 'Column names in the result, in order.'}, 'returned': {'type': 'number', 'description': 'Rows on this page â\x80\x94 fewer than limit when the 10,000-character row budget or the end of the result ends it early.'}, 'truncated': {'type': 'boolean', 'description': 'True when result rows exist after this page, including rows past the row cap that next_offset cannot reach.'}, 'next_offset': {'type': ['number', 'null'], 'description': 'offset for the next page; null when no page follows (end of the result, or the row cap reached).'}}, 'additionalProperties': False}

{'type': 'object', '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'gene': {'anyOf': [{'type': 'string', 'minLength': 2, 'description': 'Gene â\x80\x94 HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene.'}, {'type': 'string', 'maxLength': 0, 'description': 'Blank â\x80\x94 the gene is treated as omitted.'}], 'description': 'Gene â\x80\x94 HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted.'}, 'region': {'anyOf': [{'type': 'string', 'const': ''}, {'type': 'string', 'pattern': '^(?:chr)?[0-9A-Z]+-\\d+-\\d+$', 'description': 'Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852) on chromosome 1â\x80\x9322, X, or Y, optional chr prefix.'}], 'description': 'Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852): chromosome 1â\x80\x9322, X, or Y with an optional chr prefix (mitochondrial regions are not served) and a span (stop â\x88\x92 start) under 2,500,000 bp. Mutually exclusive with gene and transcript_id.'}, 'dataset': {'enum': ['gnomad_r4', 'gnomad_r3', 'gnomad_r2_1', 'exac'], 'type': 'string', 'description': 'gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.'}, 'transcript_id': {'type': 'string', 'description': 'Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted.'}, 'coverage_source': {'enum': ['exome', 'genome'], 'type': 'string', 'description': 'Restrict to one coverage track. Omit to return every available track.'}, 'reference_genome': {'enum': ['GRCh38', 'GRCh37'], 'type': 'string', '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.'}}, 'additionalProperties': False}

{'type': 'object', 'anyOf': [{'not': {'required': ['error']}, 'required': ['target', 'target_kind', 'summaries', 'dataset', 'reference_genome']}, {'required': ['error']}], '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'error': {'type': 'object', 'required': ['code', 'message'], 'properties': {'code': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991, 'description': 'JSON-RPC error code for this failure.'}, 'data': {'type': 'object', 'properties': {'reason': {'type': 'string', 'examples': ['invalid_target', 'incoherent_build', 'invalid_region', 'region_too_large', 'mitochondrial_unsupported', 'graphql_error', 'upstream_unavailable', 'upstream_timeout', 'upstream_access', 'invalid_upstream_response'], '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 1â\x80\x9322, 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.'}, 'recovery': {'type': 'object', 'required': ['hint'], 'properties': {'hint': {'type': 'string'}}, 'description': 'Actionable next step for the caller.', 'additionalProperties': {}}, 'retryable': {'type': 'boolean', 'description': 'Whether retrying may succeed.'}}, 'additionalProperties': {}}, 'message': {'type': 'string', 'description': 'Human-readable description of what went wrong.'}}, 'description': 'Present when the call failed. Absent on success.', 'additionalProperties': {}}, 'notice': {'type': 'string', 'description': 'Guidance when no coverage data is available for the target.'}, 'target': {'type': 'string', 'description': 'The resolved target (gene symbol/ID, transcript ID, or region) the coverage describes.'}, 'dataset': {'type': 'string', 'description': 'Effective gnomAD dataset.'}, 'summaries': {'type': 'array', 'items': {'type': 'object', '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'], 'properties': {'source': {'enum': ['exome', 'genome'], 'type': 'string', 'description': 'Which gnomAD coverage track this summary covers.'}, 'positions': {'type': 'number', 'description': 'Number of base positions summarized across the target.'}, 'mean_depth': {'type': ['number', 'null'], 'description': 'Mean read depth averaged across positions; null when no data.'}, 'median_depth': {'type': ['number', 'null'], 'description': 'Median read depth across positions; null when no data.'}, 'fraction_over_1': {'type': ['number', 'null'], 'description': 'Mean fraction of samples covered at â\x89¥1Ã\x97; null when no data.'}, 'fraction_over_5': {'type': ['number', 'null'], 'description': 'Mean fraction of samples covered at â\x89¥5Ã\x97; null when no data.'}, 'fraction_over_10': {'type': ['number', 'null'], 'description': 'Mean fraction of samples covered at â\x89¥10Ã\x97; null when no data.'}, 'fraction_over_15': {'type': ['number', 'null'], 'description': 'Mean fraction of samples covered at â\x89¥15Ã\x97; null when no data.'}, 'fraction_over_20': {'type': ['number', 'null'], 'description': 'Mean fraction of samples covered at â\x89¥20Ã\x97; null when no data.'}, 'fraction_over_25': {'type': ['number', 'null'], 'description': 'Mean fraction of samples covered at â\x89¥25Ã\x97; null when no data.'}, 'fraction_over_30': {'type': ['number', 'null'], 'description': 'Mean fraction of samples covered at â\x89¥30Ã\x97; null when no data.'}, 'fraction_over_50': {'type': ['number', 'null'], 'description': 'Mean fraction of samples covered at â\x89¥50Ã\x97; null when no data.'}, 'fraction_over_100': {'type': ['number', 'null'], 'description': 'Mean fraction of samples covered at â\x89¥100Ã\x97; null when no data.'}}, 'description': 'Aggregate coverage for one callset track over the target.', 'additionalProperties': False}, 'description': 'Per-track coverage summaries (exome and/or genome).'}, 'target_kind': {'enum': ['gene', 'transcript', 'region'], 'type': 'string', 'description': 'Which target type was queried.'}, 'reference_genome': {'type': 'string', 'description': 'Effective reference build.'}}, 'additionalProperties': False}

{'type': 'object', '$schema': 'https://json-schema.org/draft/2020-12/schema', 'required': ['gene'], 'properties': {'gene': {'type': 'string', 'minLength': 2, 'description': 'Gene â\x80\x94 HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene.'}, 'dataset': {'enum': ['gnomad_r4', 'gnomad_r3', 'gnomad_r2_1', 'exac'], 'type': 'string', 'description': 'gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.'}, 'reference_genome': {'enum': ['GRCh38', 'GRCh37'], 'type': 'string', '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.'}}, 'additionalProperties': False}

{'type': 'object', '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']}], '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'pli': {'anyOf': [{'type': 'number', 'maximum': 1, 'minimum': 0}, {'type': 'null'}], 'description': 'pLI â\x80\x94 probability of LoF intolerance; >0.9 intolerant. Null when unavailable.'}, 'error': {'type': 'object', 'required': ['code', 'message'], 'properties': {'code': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991, 'description': 'JSON-RPC error code for this failure.'}, 'data': {'type': 'object', 'properties': {'reason': {'type': 'string', 'examples': ['gene_not_found', 'incoherent_build', 'invalid_constraint_data', 'graphql_error', 'upstream_unavailable', 'upstream_timeout', 'upstream_access', 'invalid_upstream_response'], '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.'}, 'recovery': {'type': 'object', 'required': ['hint'], 'properties': {'hint': {'type': 'string'}}, 'description': 'Actionable next step for the caller.', 'additionalProperties': {}}, 'retryable': {'type': 'boolean', 'description': 'Whether retrying may succeed.'}}, 'additionalProperties': {}}, 'message': {'type': 'string', 'description': 'Human-readable description of what went wrong.'}}, 'description': 'Present when the call failed. Absent on success.', 'additionalProperties': {}}, 'lof_z': {'type': ['number', 'null'], 'description': 'LoF constraint Z-score. Null when unavailable.'}, 'mis_z': {'type': ['number', 'null'], 'description': 'Missense constraint Z-score. Null when unavailable.'}, 'syn_z': {'type': ['number', 'null'], 'description': 'Synonymous constraint Z-score. Null when unavailable.'}, 'oe_lof': {'anyOf': [{'type': 'number', 'minimum': 0}, {'type': 'null'}], 'description': 'Non-negative observed/expected LoF ratio. Null when unavailable.'}, 'oe_mis': {'anyOf': [{'type': 'number', 'minimum': 0}, {'type': 'null'}], 'description': 'Observed/expected missense ratio. Null when unavailable.'}, 'oe_syn': {'anyOf': [{'type': 'number', 'minimum': 0}, {'type': 'null'}], 'description': 'Observed/expected synonymous ratio. Null when unavailable.'}, 'symbol': {'type': 'string', 'description': 'HGNC gene symbol.'}, 'dataset': {'type': 'string', 'description': 'Effective gnomAD dataset.'}, 'exp_lof': {'anyOf': [{'type': 'number', 'minimum': 0}, {'type': 'null'}], 'description': 'Non-negative expected LoF variant count. Null when unavailable.'}, 'exp_mis': {'anyOf': [{'type': 'number', 'minimum': 0}, {'type': 'null'}], 'description': 'Non-negative expected missense count. Null when unavailable.'}, 'exp_syn': {'anyOf': [{'type': 'number', 'minimum': 0}, {'type': 'null'}], 'description': 'Non-negative expected synonymous count. Null when unavailable.'}, 'gene_id': {'type': 'string', 'description': 'Ensembl gene ID resolved for the gene.'}, 'obs_lof': {'anyOf': [{'type': 'number', 'minimum': 0}, {'type': 'null'}], 'description': 'Non-negative observed LoF variant count. Null when unavailable.'}, 'obs_mis': {'anyOf': [{'type': 'number', 'minimum': 0}, {'type': 'null'}], 'description': 'Non-negative observed missense count. Null when unavailable.'}, 'obs_syn': {'anyOf': [{'type': 'number', 'minimum': 0}, {'type': 'null'}], 'description': 'Non-negative observed synonymous count. Null when unavailable.'}, 'oe_lof_lower': {'anyOf': [{'type': 'number', 'minimum': 0}, {'type': 'null'}], 'description': 'LOEUF confidence-interval lower bound. Null when unavailable.'}, 'oe_lof_upper': {'anyOf': [{'type': 'number', 'minimum': 0}, {'type': 'null'}], 'description': 'LOEUF (oe_lof_upper) â\x80\x94 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.'}, 'constraint_flags': {'type': 'array', 'items': {'type': 'string'}, 'description': 'Caveat flags gnomAD attaches to the geneâ\x80\x99s constraint (e.g. no_exp_lof, mis_too_many, syn_outlier); empty when none, and always empty on exac, where ExAC publishes no flags.'}, 'reference_genome': {'type': 'string', 'description': 'Effective reference build.'}, 'constraint_release': {'type': 'string', '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.'}}, 'additionalProperties': False}

{'type': 'object', '$schema': 'https://json-schema.org/draft/2020-12/schema', 'required': ['variants'], 'properties': {'dataset': {'enum': ['gnomad_r4', 'gnomad_r3', 'gnomad_r2_1', 'exac'], 'type': 'string', 'description': 'gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.'}, 'variants': {'type': 'array', 'items': {'type': 'string', 'minLength': 1, 'description': 'Variant ID â\x80\x94 chrom-pos-ref-alt (1-based, e.g. 1-55051215-G-GA) on chromosome 1â\x80\x9322, 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.'}, 'maxItems': 25, 'minItems': 1, 'description': '1â\x80\x9325 variant IDs (chrom-pos-ref-alt or rsID) to look up in one batched call.'}, 'reference_genome': {'enum': ['GRCh38', 'GRCh37'], 'type': 'string', '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.'}}, 'additionalProperties': False}

{'type': 'object', 'anyOf': [{'not': {'required': ['error']}, 'required': ['found', 'failed', 'dataset', 'reference_genome']}, {'required': ['error']}], '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'error': {'type': 'object', 'required': ['code', 'message'], 'properties': {'code': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991, 'description': 'JSON-RPC error code for this failure.'}, 'data': {'type': 'object', 'properties': {'reason': {'type': 'string', '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'], '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.'}, 'recovery': {'type': 'object', 'required': ['hint'], 'properties': {'hint': {'type': 'string'}}, 'description': 'Actionable next step for the caller.', 'additionalProperties': {}}, 'retryable': {'type': 'boolean', 'description': 'Whether retrying may succeed.'}}, 'additionalProperties': {}}, 'message': {'type': 'string', 'description': 'Human-readable description of what went wrong.'}}, 'description': 'Present when the call failed. Absent on success.', 'additionalProperties': {}}, 'found': {'type': 'array', 'items': {'type': 'object', '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'], 'properties': {'ac': {'type': 'number', 'description': 'Overall allele count across carried callset(s).'}, 'af': {'type': ['number', 'null'], 'description': 'Overall allele frequency; null when an is 0.'}, 'an': {'type': 'number', 'description': 'Overall allele number across carried callset(s).'}, 'flags': {'type': 'array', 'items': {'type': 'string'}, 'description': 'Quality flags (e.g. lcr, segdup, lc_lof).'}, 'rsids': {'type': 'array', 'items': {'type': 'string'}, 'description': 'dbSNP rsIDs for this variant.'}, 'source': {'type': 'array', 'items': {'enum': ['exome', 'genome'], 'type': 'string'}, 'description': 'Which gnomAD callset(s) carry this variant.'}, 'clinvar': {'anyOf': [{'type': 'object', 'required': ['clinical_significance', 'review_status', 'gold_stars', 'clinvar_variation_id'], 'properties': {'gold_stars': {'type': ['number', 'null'], 'description': 'ClinVar 0â\x80\x934 star review rating.'}, 'review_status': {'type': ['string', 'null'], 'description': 'ClinVar review status text.'}, 'clinvar_variation_id': {'type': ['string', 'null'], 'description': 'ClinVar VariationID.'}, 'clinical_significance': {'type': ['string', 'null'], 'description': 'ClinVar clinical significance (e.g. Pathogenic, Likely benign); null when no entry.'}}, 'description': 'Joined ClinVar significance from gnomAD. Null when the variant has no ClinVar entry.', 'additionalProperties': False}, {'type': 'null'}], 'description': 'ClinVar annotation, or null when no entry exists.'}, 'dataset': {'type': 'string', 'description': 'Effective gnomAD dataset.'}, 'in_silico': {'type': 'array', 'items': {'type': 'object', 'required': ['id', 'value', 'annotation'], 'properties': {'id': {'type': 'string', 'description': 'Predictor name. Ids vary by dataset â\x80\x94 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.'}, 'value': {'type': ['number', 'null'], 'description': 'Predictor score; null when not provided for this variant, or when gnomAD gave text with no number (the text is then in annotation).'}, 'annotation': {'type': ['string', 'null'], 'description': 'Text gnomAD attaches to the score â\x80\x94 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.'}}, 'description': 'One in-silico predictor score.', 'additionalProperties': False}, 'description': 'In-silico predictor scores present for this variant.'}, 'variant_id': {'type': 'string', 'description': 'Resolved chrom-pos-ref-alt variant ID.'}, 'consequence': {'type': ['string', 'null'], 'description': 'Worst/transcript VEP consequence term; null when none.'}, 'gene_symbol': {'type': ['string', 'null'], 'description': 'Gene symbol for the reported consequence; null when none.'}, 'populations': {'type': 'array', 'items': {'type': 'object', 'required': ['id', 'source', 'ac', 'an', 'af', 'homozygote_count', 'hemizygote_count'], 'properties': {'ac': {'type': 'number', 'description': 'Allele count in this group.'}, 'af': {'type': ['number', 'null'], 'description': 'Allele frequency (ac/an); null when an is 0.'}, 'an': {'type': 'number', 'description': 'Allele number (called chromosomes) in this group.'}, 'id': {'type': 'string', 'description': 'Genetic-ancestry group: afr, amr, asj, eas, fin, mid, nfe, sas, remaining, or ami (genomes only).'}, 'source': {'enum': ['exome', 'genome'], 'type': 'string', 'description': 'Which gnomAD callset this group vector came from.'}, 'hemizygote_count': {'type': ['number', 'null'], 'description': 'Hemizygote count (X/Y only); null otherwise.'}, 'homozygote_count': {'type': 'number', 'description': 'Homozygote count in this group.'}}, 'description': 'One genetic-ancestry group AC/AN/AF vector.', 'additionalProperties': False}, 'description': 'Per-ancestry frequency vector â\x80\x94 never collapsed to a single global AF.'}, 'transcript_id': {'type': ['string', 'null'], 'description': 'Transcript the consequence is on; null when none.'}, 'hemizygote_count': {'type': ['number', 'null'], 'description': 'Overall hemizygote count (X/Y only); null otherwise.'}, 'homozygote_count': {'type': 'number', 'description': 'Overall homozygote count.'}, 'reference_genome': {'type': 'string', 'description': 'Reference build the record is on (GRCh38 or GRCh37).'}, 'clinvar_unavailable': {'type': 'boolean', 'description': 'True when the optional ClinVar resolver failed; false when no entry exists.'}}, 'description': 'Full population record for one variant.', 'additionalProperties': False}, 'description': 'Variants resolved to a population record.'}, 'failed': {'type': 'array', 'items': {'type': 'object', 'required': ['variant', 'error', 'reason', 'recovery'], 'properties': {'error': {'type': 'string', 'description': 'What went wrong for this ID.'}, 'reason': {'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', 'description': "Why this ID failed â\x80\x94 a reason declared in this tool's error contract. Branch on it rather than on the message."}, 'variant': {'type': 'string', 'description': 'The input ID that failed to resolve.'}, 'recovery': {'type': 'string', 'description': 'The next step for this ID â\x80\x94 the recovery hint declared for its reason.'}, 'candidates': {'type': 'array', 'items': {'type': 'string'}, 'description': 'Concrete variant IDs to retry when an rsID is ambiguous.'}}, 'description': 'One failed input ID, why it failed, and what to do next.', 'additionalProperties': False}, 'description': 'Per-item failures, in input order: malformed IDs, variants absent from the dataset, or upstream errors â\x80\x94 each with its reason and recovery hint.'}, 'notice': {'type': 'string', 'description': 'Non-fatal notice when optional ClinVar annotation was unavailable.'}, 'dataset': {'type': 'string', 'description': 'Effective gnomAD dataset used for the batch.'}, 'reference_genome': {'type': 'string', 'description': 'Effective reference build used for the batch.'}}, 'additionalProperties': False}

{'type': 'object', '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'gene': {'anyOf': [{'type': 'string', 'minLength': 2, 'description': 'Gene â\x80\x94 HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene.'}, {'type': 'string', 'maxLength': 0, 'description': 'Blank â\x80\x94 the gene is treated as omitted.'}], 'description': 'Gene â\x80\x94 HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted.'}, 'max_af': {'type': 'number', 'maximum': 1, 'minimum': 0, 'description': 'Keep only variants with allele frequency â\x89¤ this value (0â\x80\x931). Variants with null AF are always kept.'}, 'region': {'anyOf': [{'type': 'string', 'const': ''}, {'type': 'string', 'pattern': '^(?:chr)?[0-9A-Z]+-\\d+-\\d+$', 'description': 'Genomic region chrom-start-stop (1-based inclusive, e.g. 13-32315474-32400266) on chromosome 1â\x80\x9322, X, or Y, optional chr prefix.'}], 'description': 'Genomic region chrom-start-stop (1-based inclusive, e.g. 13-32315474-32400266): chromosome 1â\x80\x9322, X, or Y with an optional chr prefix (mitochondrial regions are not served), a span (stop â\x88\x92 start) under 2,500,000 bp, and at most ~30,000 variants. Mutually exclusive with gene and transcript_id.'}, 'dataset': {'enum': ['gnomad_r4', 'gnomad_r3', 'gnomad_r2_1', 'exac'], 'type': 'string', 'description': 'gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.'}, 'canvas_id': {'type': 'string', 'pattern': '^[A-Za-z0-9_-]{10}$', '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 â\x80\x94 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.'}, 'transcript_id': {'type': 'string', 'description': 'Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted.'}, 'reference_genome': {'enum': ['GRCh38', 'GRCh37'], 'type': 'string', '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.'}, 'consequence_class': {'enum': ['lof', 'missense', 'synonymous', 'other'], 'type': 'string', 'description': 'Keep only variants in this consequence class. Omit to return all classes.'}}, 'additionalProperties': False}

{'type': 'object', 'anyOf': [{'not': {'required': ['error']}, 'required': ['preview', 'canvas_id', 'table_name', 'spilled', 'total', 'dataset', 'reference_genome']}, {'required': ['error']}], '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'error': {'type': 'object', 'required': ['code', 'message'], 'properties': {'code': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991, 'description': 'JSON-RPC error code for this failure.'}, 'data': {'type': 'object', 'properties': {'reason': {'type': 'string', 'examples': ['invalid_target', 'incoherent_build', 'invalid_region', 'region_too_large', 'mitochondrial_unsupported', 'graphql_error', 'upstream_unavailable', 'upstream_timeout', 'upstream_access', 'invalid_upstream_response'], '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 1â\x80\x9322, 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.'}, 'recovery': {'type': 'object', 'required': ['hint'], 'properties': {'hint': {'type': 'string'}}, 'description': 'Actionable next step for the caller.', 'additionalProperties': {}}, 'retryable': {'type': 'boolean', 'description': 'Whether retrying may succeed.'}}, 'additionalProperties': {}}, 'message': {'type': 'string', 'description': 'Human-readable description of what went wrong.'}}, 'description': 'Present when the call failed. Absent on success.', 'additionalProperties': {}}, 'total': {'type': 'number', 'description': 'Total matching variants, including any beyond the preview.'}, 'notice': {'type': 'string', 'description': 'Guidance when no variants matched, when the canvas is disabled and the preview is capped, and â\x80\x94 when a table was staged â\x80\x94 its name with the next steps: gnomad_dataframe_describe, then gnomad_dataframe_query.'}, 'dataset': {'type': 'string', 'description': 'Effective gnomAD dataset.'}, 'preview': {'type': 'array', 'items': {'type': 'object', 'required': ['variant_id', 'af', 'ac', 'an', 'consequence', 'consequence_class', 'homozygote_count', 'source', 'flags'], 'properties': {'ac': {'type': 'number', 'description': 'Allele count (joint across carried callsets).'}, 'af': {'type': ['number', 'null'], 'description': 'Allele frequency computed from joint allele counts; null when uncomputable.'}, 'an': {'type': 'number', 'description': 'Allele number (joint sum across carried callsets).'}, 'flags': {'type': 'string', 'description': 'Quality flags, pipe-joined (empty when none).'}, 'source': {'type': 'string', 'description': 'Carried callset(s), pipe-joined (e.g. exome|genome).'}, 'variant_id': {'type': 'string', 'description': 'chrom-pos-ref-alt variant ID.'}, 'consequence': {'type': ['string', 'null'], 'description': 'VEP consequence term; null when none.'}, 'homozygote_count': {'type': 'number', 'description': 'Homozygote count (joint across callsets).'}, 'consequence_class': {'enum': ['lof', 'missense', 'synonymous', 'other'], 'type': 'string', 'description': 'Bucketed consequence class.'}}, 'description': 'One gene-variant row â\x80\x94 also the canvas table column set.', 'additionalProperties': False}, 'description': 'Inline preview rows â\x80\x94 the immediate answer; every matching variant unless spilled.'}, 'spilled': {'type': 'boolean', 'description': 'True when the result exceeded the inline preview budget, so the preview holds only the first rows and table_name holds them all.'}, 'canvas_id': {'type': 'string', 'description': 'Canvas holding table_name (or the canvas_id you supplied) â\x80\x94 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.'}, 'table_name': {'type': 'string', 'description': 'Canvas table this call staged (gene_variants), holding every matching variant â\x80\x94 inspect it with gnomad_dataframe_describe, then query it with gnomad_dataframe_query. Empty when this call staged no table.'}, 'reference_genome': {'type': 'string', 'description': 'Effective reference build.'}}, 'additionalProperties': False}

{'type': 'object', '$schema': 'https://json-schema.org/draft/2020-12/schema', 'required': ['gene'], 'properties': {'gene': {'type': 'string', 'minLength': 2, 'description': 'Gene HGNC symbol (e.g. PCSK9). ClinVar indexes HGNC symbols only â\x80\x94 Ensembl gene IDs (ENSGâ\x80¦) are not resolved here, unlike the other gnomAD tools; resolve one to its symbol via ensembl_lookup_gene.'}, 'limit': {'type': 'integer', 'default': 500, 'maximum': 500, 'minimum': 1, 'description': 'ClinVar records to fetch in this window (1â\x80\x93500). Counted before the clinical_significance and min_review_stars filters, so a window can return fewer rows.'}, 'offset': {'type': 'integer', 'default': 0, 'maximum': 2147483647, 'minimum': 0, 'description': 'Zero-based position of the first ClinVar record in this window. Pass next_offset from the previous call to continue.'}, 'canvas_id': {'type': 'string', 'pattern': '^[A-Za-z0-9_-]{10}$', '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 â\x80\x94 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.'}, 'min_review_stars': {'type': 'integer', 'maximum': 4, 'minimum': 0, 'description': 'Keep only variants with at least this gold-star review rating (0â\x80\x934).'}, 'clinical_significance': {'type': 'string', '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.'}}, 'additionalProperties': False}

{'type': 'object', 'anyOf': [{'not': {'required': ['error']}, 'required': ['preview', 'canvas_id', 'table_name', 'spilled', 'total', 'total_found', 'truncated', 'next_offset', 'unavailable_ids']}, {'required': ['error']}], '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'error': {'type': 'object', 'required': ['code', 'message'], 'properties': {'code': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991, 'description': 'JSON-RPC error code for this failure.'}, 'data': {'type': 'object', 'properties': {'reason': {'type': 'string', 'examples': ['upstream_unavailable', 'upstream_timeout', 'upstream_access', 'invalid_upstream_response'], '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.'}, 'recovery': {'type': 'object', 'required': ['hint'], 'properties': {'hint': {'type': 'string'}}, 'description': 'Actionable next step for the caller.', 'additionalProperties': {}}, 'retryable': {'type': 'boolean', 'description': 'Whether retrying may succeed.'}}, 'additionalProperties': {}}, 'message': {'type': 'string', 'description': 'Human-readable description of what went wrong.'}}, 'description': 'Present when the call failed. Absent on success.', 'additionalProperties': {}}, 'total': {'type': 'number', 'description': 'Rows in this window that passed the filters, including any beyond the preview.'}, 'notice': {'type': 'string', '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.'}, 'preview': {'type': 'array', 'items': {'type': 'object', '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'], 'properties': {'rsids': {'type': 'string', '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.'}, 'title': {'type': 'string', 'description': 'Variant title (HGVS expression).'}, 'obj_type': {'type': 'string', 'description': 'Variant object type (e.g. single nucleotide variant).'}, 'accession': {'type': 'string', 'description': 'ClinVar accession (e.g. VCV004855003).'}, 'conditions': {'type': 'string', 'description': 'Associated conditions/traits, semicolon-joined.'}, 'gold_stars': {'type': 'number', 'description': '0â\x80\x934 star review rating derived from review status.'}, 'review_status': {'type': ['string', 'null'], 'description': 'ClinVar review-status text; null when none.'}, 'canonical_spdi': {'type': ['string', 'null'], '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.'}, 'last_evaluated': {'type': ['string', 'null'], 'description': 'Date the classification was last evaluated; null when unknown.'}, 'protein_change': {'type': 'string', 'description': 'Protein change(s), comma-joined as ClinVar reports them.'}, 'submission_count': {'type': 'number', 'description': 'Number of submitted (SCV) records.'}, 'grch38_variant_id': {'type': ['string', 'null'], '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.'}, 'clinvar_variation_id': {'type': 'string', 'description': 'ClinVar VariationID (uid).'}, 'clinical_significance': {'type': ['string', 'null'], 'description': 'Germline classification (e.g. Pathogenic); null when none.'}, 'molecular_consequences': {'type': 'string', 'description': 'Molecular consequences, semicolon-joined.'}}, 'description': 'One ClinVar variant row â\x80\x94 also the canvas table column set.', 'additionalProperties': False}, 'description': "Inline preview rows â\x80\x94 the immediate answer; the window's every row unless spilled."}, 'spilled': {'type': 'boolean', '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."}, 'canvas_id': {'type': 'string', 'description': 'Canvas holding table_name (or the canvas_id you supplied) â\x80\x94 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.'}, 'truncated': {'type': 'boolean', 'description': 'True when ClinVar records remain past this window; continue with next_offset.'}, 'table_name': {'type': 'string', 'description': "Canvas table this call staged (clinvar_variants), holding this window's rows â\x80\x94 inspect it with gnomad_dataframe_describe, then query it with gnomad_dataframe_query. Empty when this call staged no table."}, 'next_offset': {'type': ['number', 'null'], 'description': 'offset for the next window; null when this window reaches the end.'}, 'total_found': {'type': 'number', 'description': 'ClinVar records matching the gene and filter terms across every window, counted before the post-fetch significance and star filters.'}, 'unavailable_ids': {'type': 'array', 'items': {'type': 'string'}, 'description': 'VariationIDs in this window that ClinVar returned no summary for, so they have no row; empty when none.'}}, 'additionalProperties': False}