io.github.cyanheads/gnomad-genetics-mcp-server
io.github.cyanheads/gnomad-genetics-mcp-server
MCP Bill of Materials
A machine-readable inventory of what this server exposes and depends on: tools with their effects, transports, packages, findings and provenance (schema version 1.0). Third-party text in it is escaped. Also available from the REST API at /api/v1/servers/4d07c0f1-6f72-4089-bd63-0d8d8188d23f/mcbom.
MCP Bill of Materials
root{21}
schema_version: "1.0"
bom_format: "squatch-mcbom"
generator{3}
name: "squatch-mcp"
classifier_version: "rules_v1@2026-10-11.1"
unicode_version: "18.0.0"
server{7}
name: "io.github.cyanheads/gnomad-genetics-mcp-server"
title: null
description: "Ancestry allele frequencies, LoF constraint, variant lists, and coverage from gnomAD, with ClinVar."
version: "0.6.0"
homepage_url: null
source: "official_registry"
upstream_status: "active"
publisher{4}
namespace: "io.github.cyanheads"
display_name: "io.github.cyanheads"
type: "registry_namespace"
status: "unclaimed"
organization: null
repository{5}
url: "https://github.com/cyanheads/gnomad-genetics-mcp-server"
provider: "github"
owner: "cyanheads"
name: "gnomad-genetics-mcp-server"
verified: false
packages[2]
0{4}
registry_type: "npm"
identifier: "@cyanheads/gnomad-genetics-mcp-server"
version: "0.6.0"
transport: "stdio"
1{4}
registry_type: "npm"
identifier: "@cyanheads/gnomad-genetics-mcp-server"
version: "0.6.0"
transport: "streamable-http"
transports[3]
0{5}
kind: "package"
type: "stdio"
endpoint_url: null
endpoint_host: null
auth_type: "unknown"
1{5}
kind: "package"
type: "streamable-http"
endpoint_url: null
endpoint_host: null
auth_type: "unknown"
2{5}
kind: "remote"
type: "streamable-http"
endpoint_url: "https://gnomad-genetics.caseyjhand.com/mcp"
endpoint_host: "gnomad-genetics.caseyjhand.com"
auth_type: "none"
auth{3}
type: "none"
authorization_servers[0]
scopes[0]
protocol{4}
era: "modern"
negotiated_version: "2026-07-28"
supported_versions[0]
transport_type: "streamable-http"
tools[8]
0{9}
name: "gnomad_dataframe_describe"
title: "gnomad-genetics-mcp-server: dataframe describe"
effect: "READ"
effect_confidence: 0.813
capabilities[1]
0{2}
capability: "DATABASE_ACCESS"
confidence: 0.632
risk_severity: "INFO"
fingerprint: "580ce5ef6d4ae0bb2a1ea94d93889f3a7a49f494fdbd94694c61d957cb25ccb5"
input_schema_fingerprint: "19486c21fea7d87304dfcb6fffe5e2d43258532991c7026519d4a90d9639329e"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: false
1{9}
name: "gnomad_dataframe_query"
title: "gnomad-genetics-mcp-server: dataframe query"
effect: "EXECUTE"
effect_confidence: 0.869
capabilities[1]
0{2}
capability: "DATABASE_ACCESS"
confidence: 0.648
risk_severity: "CRITICAL"
fingerprint: "93429311515da4cbd024205764ed4609ca5218ab4788117b94dc0329eb93d9bb"
input_schema_fingerprint: "ae67fd685d621d16f770a05ec0feb193ea7cc2cac33f368b5acb7a3182576691"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: false
2{9}
name: "gnomad_get_coverage"
title: "gnomad-genetics-mcp-server: get coverage"
effect: "READ"
effect_confidence: 0.841
capabilities[2]
0{2}
capability: "CLOUD_INFRASTRUCTURE"
confidence: 0.53
1{2}
capability: "SENSITIVE_PERSONAL_DATA"
confidence: 0.61
risk_severity: "MEDIUM"
fingerprint: "a4440a63ffb9ef06737c04a325ec1dd12afd65725145f3eb169844669db84f51"
input_schema_fingerprint: "196471ac293f717cc487b552ee38a69cb380f1658c77b133d0e80909d553ce33"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
3{9}
name: "gnomad_get_gene_constraint"
title: "gnomad-genetics-mcp-server: get gene constraint"
effect: "READ"
effect_confidence: 0.841
capabilities[0]
risk_severity: "INFO"
fingerprint: "0f698bf3bcf149e09a5a548710099aaef902da01b2bed5c20c3be9bd1f7b67d1"
input_schema_fingerprint: "ca21935bf7b8ca931c1d4c231b71036d831c4ca9432c9bac1a1ddb681849b617"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
4{9}
name: "gnomad_get_variant"
title: "gnomad-genetics-mcp-server: get variant"
effect: "READ"
effect_confidence: 0.841
capabilities[1]
0{2}
capability: "SENSITIVE_PERSONAL_DATA"
confidence: 0.708
risk_severity: "MEDIUM"
fingerprint: "a0e6255ff945e3d2b7acc6b83fea555a7f97acab9c0c7b0b7724872813beeb05"
input_schema_fingerprint: "745457fd7a305acbb578d83ad2a7539c557cef30165eb82d03b2692ffc0688bf"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
5{9}
name: "gnomad_get_variant_cooccurrence"
title: "gnomad-genetics-mcp-server: get variant cooccurrence"
effect: "READ"
effect_confidence: 0.813
capabilities[1]
0{2}
capability: "SENSITIVE_PERSONAL_DATA"
confidence: 0.708
risk_severity: "MEDIUM"
fingerprint: "736a24762ed32464657220631508ad9b41088b494f8295bca121b18ca97c966d"
input_schema_fingerprint: "fe114d2280101a6baa84f7622a077c72950f28a0a4debf02314a0c5ffa335500"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
6{9}
name: "gnomad_list_gene_variants"
title: "gnomad-genetics-mcp-server: list gene variants"
effect: "READ"
effect_confidence: 0.841
capabilities[1]
0{2}
capability: "CLOUD_INFRASTRUCTURE"
confidence: 0.53
risk_severity: "INFO"
fingerprint: "e91b3673bee59af90487beaa6181e6c1cde4186fb15a9ff7ae2bc385fd5dd5f6"
input_schema_fingerprint: "ed3349d82ffa354f9399362a0c390f85e851d378c01f5e0f1c7f4a0a292c3d3a"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
7{9}
name: "gnomad_search_clinvar"
title: "gnomad-genetics-mcp-server: search clinvar"
effect: "READ"
effect_confidence: 0.841
capabilities[2]
0{2}
capability: "HEALTH"
confidence: 0.687
1{2}
capability: "SENSITIVE_PERSONAL_DATA"
confidence: 0.796
risk_severity: "MEDIUM"
fingerprint: "7ae05416bcc17d925d1fcbac1287b0f2fa766fa85de2cd9c1d5a078ea73a1416"
input_schema_fingerprint: "384ee006848a3f8aa58e2d123a2a712a1a004c3ff76c4cf4f03318effa7b44f7"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
resources[4]
0{4}
key: "skill://gnomad-genetics-guide/SKILL.md"
kind: "resource"
mime_type: "text/markdown"
fingerprint: "a9acbdcbe737888b5af2da2275265fa8f1d2efee6e504aabe3a514ce276e0015"
1{4}
key: "gnomad://gene/{dataset}/{gene}/constraint"
kind: "template"
mime_type: "application/json"
fingerprint: "8f90d069ef5083fa0b361dcff8545f3082c007b2f3ef500280d5708234e8aef8"
2{4}
key: "gnomad://variant/{dataset}/{variantId}"
kind: "template"
mime_type: "application/json"
fingerprint: "ab68cc26f1d9b7ff6429c022f6df75c8cf11daebbdec8aea3167d84fea61b566"
3{4}
key: "skill://{+path}"
kind: "template"
mime_type: null
fingerprint: "9777dc7f1cf468158c157032a0ccebf9b50270f4e8753af9ccaf2fe99890ccf0"
prompts[1]
0{2}
name: "gnomad_variant_triage"
fingerprint: "89fa3f975b2d7e401002141a4283f1d1018dc94225a71ef3135c247550908c5b"
extensions[1]
0: "io.modelcontextprotocol/skills"
data{6}
privacy_completeness: "not_provided"
data_categories[0]
ai_training: null
retention_policy: null
processing_regions[0]
subprocessors[0]
external_integrations[1]
0{3}
host: "gnomad-genetics.caseyjhand.com"
registrable_domain: "caseyjhand.com"
source: "transport"
findings[7]
0{6}
check_id: "SQ-SERVER-AUTH-NONE-WRITE"
category: "authentication"
severity: "MEDIUM"
title: "State-changing tools available without authentication"
subject_type: "server"
subject_name: null
1{6}
check_id: "SQ-TOOL-ANNOTATION-UNDERCLAIM"
category: "annotations"
severity: "HIGH"
title: "Annotations understate what the tool does"
subject_type: "tool"
subject_name: "gnomad_dataframe_query"
2{6}
check_id: "SQ-TOOL-EXFIL-DIRECTIVE"
category: "prompt_injection"
severity: "HIGH"
title: "Asks the AI model to pass conversation data or secrets"
subject_type: "tool"
subject_name: "gnomad_list_gene_variants"
3{6}
check_id: "SQ-TOOL-EXFIL-DIRECTIVE"
category: "prompt_injection"
severity: "HIGH"
title: "Asks the AI model to pass conversation data or secrets"
subject_type: "tool"
subject_name: "gnomad_search_clinvar"
4{6}
check_id: "SQ-TOOL-EXFIL-SHAPED-PARAM"
category: "schema"
severity: "INFO"
title: "Free-text parameter commonly used to collect conversation data"
subject_type: "tool"
subject_name: "gnomad_get_coverage"
5{6}
check_id: "SQ-TOOL-EXFIL-SHAPED-PARAM"
category: "schema"
severity: "LOW"
title: "Free-text parameter commonly used to collect conversation data"
subject_type: "tool"
subject_name: "gnomad_list_gene_variants"
6{6}
check_id: "SQ-TOOL-SENSITIVE-PATH-REFERENCE"
category: "prompt_injection"
severity: "HIGH"
title: "References credential or key locations"
subject_type: "tool"
subject_name: "gnomad_search_clinvar"
trust{9}
registry_namespace: "verified_upstream"
publisher_identity: "unverified"
organization: "unverified"
domain: "unverified"
repository: "unverified"
source_provenance: "partial"
security_scan: "findings_detected"
privacy_transparency: "not_provided"
monitoring: "active"
provenance{4}
registry_name: "io.github.cyanheads/gnomad-genetics-mcp-server"
registry_content_sha256: "17d8eadf85546c1e2e5a5c5213bd22093a77a9bc339d6dbbdb1983602be4e6ae"
scan_snapshot_fingerprint: "fbd6c71907e76eadd0bcca4f4d24596aeb4954ed4a665417e9652fea5252f763"
scanner_version: "1.0.0"
timestamps{4}
generated_at: "2026-11-15T02:15:02.063Z"
observed_at: "2026-11-13T05:42:11.099+00:00"
registry_published_at: "2026-11-04T06:29:49.76895+00:00"
registry_updated_at: null