{"name":"net.genebe/genebe-mcp","slug":"genebe-mcp","title":"GeneBe","description":"Annotate and classify human genetic variants with GeneBe (ACMG, gnomAD, ClinVar). Research use only.","url":"https://mcp.market/server/genebe-mcp","rating":null,"grade":"A","score":87,"certified":false,"status":"active","category":"other","tags":[],"presence":{"score":23,"stars":0,"forks":0,"downloads_week":null,"last_push_at":"2026-10-22T13:06:28.000Z","license":"MIT"},"uptime":{"percent":100,"checks":28,"ok":28,"last_checked_at":"2026-11-04T07:35:58.179Z","last_ok_at":"2026-11-04T07:35:58.179Z","latency_ms":1096},"claimed":false,"transport":"remote","callable_via_gateway":true,"default_price_micros":0,"repository":"https://github.com/genebe-net/genebe-mcp","website":"https://genebe.net","version":"0.1.0","remotes":[{"type":"streamable-http","url":"https://mcp.genebe.net/v1/mcp"}],"packages":[],"tools":[{"name":"annotate_variant","description":"Annotate and classify one human genetic variant using GeneBe.\n\nStart here for any question about a variant (what is it, is it pathogenic/benign, how common is it).\nReturns the ACMG verdict with points and criteria, population frequency (gnomAD), predictor scores\n(REVEL, AlphaMissense, SpliceAI, ...), ClinVar status, transcript consequences, and links to the\nGeneBe page to cite. Research use only; not a diagnosis.\n","write_action":false,"price_micros":0,"input_schema":{"type":"object","properties":{"variant":{"description":"The variant. Accepts 'chr-pos-ref-alt' (6-160585140-T-G), HGVS with transcript (NM_005577.4:c.4195A>C), rsID (rs41272110), SPDI, or 'GENE p.Thr1399Pro'.","title":"Variant","type":"string"},"genome":{"default":"hg38","description":"Genome build of coordinate input. Ignored for HGVS/rsID.","enum":["hg19","hg38","t2t"],"title":"Genome","type":"string"},"transcript":{"anyOf":[{"type":"string"},{"type":"null"}],"default":null,"description":"Force this transcript for the classification, e.g. NM_000546.6","title":"Transcript"},"gene_symbol":{"anyOf":[{"type":"string"},{"type":"null"}],"default":null,"description":"Force this gene for the classification, e.g. TP53","title":"Gene Symbol"}},"required":["variant"],"title":"annotate_variantArguments"}},{"name":"convert_variant","description":"Convert a variant written in any notation into normalized hg38 genomic coordinates.\n\nUse when you only need the chr/pos/ref/alt of a variant (for example to translate HGVS or an rsID),\nwithout annotation. Does not classify the variant; use annotate_variant for that.\n","write_action":false,"price_micros":0,"input_schema":{"type":"object","properties":{"variant":{"description":"HGVS (NM_007294.4:c.3756_3759del), rsID (rs429358), SPDI (NC_000007.14:11324573:C:T), 'chr-pos-ref-alt', or 'GENE p.Thr1700Ile'.","title":"Variant","type":"string"},"input_genome":{"default":"hg38","description":"Genome build of positional input (hg19 input is lifted to hg38).","enum":["hg19","hg38","t2t"],"title":"Input Genome","type":"string"}},"required":["variant"],"title":"convert_variantArguments"}},{"name":"explain_acmg_decision_path","description":"Explain step by step why each classification criterion did or did not apply to a variant.\n\nUse after annotate_variant when the user asks \"why was this classified that way?\". Returns an\nASCII rendering of the decision tree with the evaluated conditions. By default it explains the\ngermline ACMG verdict that annotate_variant returns; the somatic trees 'oncogenicity' (2022) and\n'acgs-uk-onco' (2025) can be requested explicitly. Research use only.\n","write_action":false,"price_micros":0,"input_schema":{"type":"object","properties":{"variant":{"description":"The variant, in any notation accepted by annotate_variant.","title":"Variant","type":"string"},"genome":{"default":"hg38","description":"Genome build of coordinate input.","enum":["hg19","hg38","t2t"],"title":"Genome","type":"string"},"tree":{"default":"germline","description":"Decision tree: 'germline' (default), 'oncogenicity' or 'acgs-uk-onco'.","title":"Tree","type":"string"},"version":{"default":"2019","description":"Tree version: germline 2019 (default), oncogenicity 2022, acgs-uk-onco 2025.","title":"Version","type":"string"}},"required":["variant"],"title":"explain_acmg_decision_pathArguments"}},{"name":"get_gene","description":"Look up a human gene: identifiers, location, MANE Select transcript, ClinGen gene-disease validity.\n\nUse for questions about a gene rather than a specific variant. Transcripts are listed with\nMANE Select first and capped; check total_transcripts.\n","write_action":false,"price_micros":0,"input_schema":{"type":"object","properties":{"gene":{"description":"Gene symbol (BRCA1), alias, HGNC id (HGNC:1100), 'entrez:672' or Ensembl id (ENSG...).","title":"Gene","type":"string"},"include_transcripts":{"default":true,"description":"Also list the gene's transcripts.","title":"Include Transcripts","type":"boolean"}},"required":["gene"],"title":"get_geneArguments"}},{"name":"get_variant_effects","description":"List a variant's predicted molecular consequences on every overlapping transcript.\n\nReturns per-transcript HGVS (c. and p.), consequence terms (e.g. missense_variant) and impact,\nmost severe and MANE Select transcripts first. Lightweight: no frequencies or classification.\n","write_action":false,"price_micros":0,"input_schema":{"type":"object","properties":{"variant":{"description":"The variant, in any notation accepted by annotate_variant.","title":"Variant","type":"string"},"genome":{"default":"hg38","description":"Genome build of coordinate input.","enum":["hg19","hg38","t2t"],"title":"Genome","type":"string"}},"required":["variant"],"title":"get_variant_effectsArguments"}},{"name":"liftover_coordinate","description":"Convert a genomic position, interval or variant between genome builds (hg19, hg38, t2t).\n\nCheck `status`: RESOLVED means one result, AMBIGUOUS means several candidates, anything else\nmeans it could not be mapped (see errors). For variants, ref/alt are rebuilt against the target\nreference and warnings such as REF_MISMATCH may apply.\n","write_action":false,"price_micros":0,"input_schema":{"type":"object","properties":{"query":{"description":"A position ('chr8:141310715'), an interval ('chr8:141310715-141310716') or a variant ('chr2-23423-A-C', HGVS, rsID).","title":"Query","type":"string"},"from_genome":{"description":"Genome build of the input.","enum":["hg19","hg38","t2t"],"title":"From Genome","type":"string"},"to_genome":{"description":"Genome build to convert to.","enum":["hg19","hg38","t2t"],"title":"To Genome","type":"string"}},"required":["query","from_genome","to_genome"],"title":"liftover_coordinateArguments"}}],"scan":{"score":87,"grade":"A","scanned_at":"2026-10-25T09:23:53.753Z","report":{"scannerVersion":"0.1.10","scannedAt":"2026-10-25T09:23:53.715Z","components":{"code":{"score":-1,"max":25,"notes":["remote-only server, no package to scan"]},"reliability":{"score":17,"max":20,"notes":["remote reachable in 2019ms"]},"poisoning":{"score":15,"max":15,"notes":["6 tool descriptions checked"]},"auth":{"score":10,"max":15,"notes":["open endpoint, read-only tools"]},"maintenance":{"score":15,"max":15,"notes":["last push 3 days ago"]},"identity":{"score":8,"max":10,"notes":["namespace and repository owner differ","GitHub account older than a year","website matches verified namespace"]}},"findings":[],"inputs":{"probes":[{"url":"https://mcp.genebe.net/v1/mcp","reachable":true,"authRequired":false,"latencyMs":2019,"serverInfo":{"name":"GeneBe","version":"0.1.0"}}],"packages":[],"repo":{"found":true,"owner":"genebe-net","repo":"genebe-mcp","archived":false,"pushedAt":"2026-10-22T13:06:28Z","stars":0,"forks":0,"openIssues":0,"ownerType":"Organization","ownerAvatarUrl":"https://avatars.githubusercontent.com/u/138305970?v=4","ownerCreatedAt":"2023-07-01T13:26:17Z","license":"MIT"},"icon":{"url":"https://genebe.net/apple-touch-icon.png?v=20260514","source":"site","width":180,"height":180},"presence":{"stars":0,"forks":0,"downloadsWeek":null,"license":"MIT","lastPushAt":"2026-10-22T13:06:28.000Z","score":23}}}},"grade_history":[],"reviews":[]}