Annotate and classify human genetic variants with GeneBe (ACMG, gnomAD, ClinVar). Research use only.
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Annotate and classify one human genetic variant using GeneBe. Start here for any question about a variant (what is it, is it pathogenic/benign, how common is it). Returns the ACMG verdict with points and criteria, population frequency (gnomAD), predictor scores (REVEL, AlphaMissense, SpliceAI, ...), ClinVar status, transcript consequences, and links to the GeneBe page to cite. Research use only; not a diagnosis.
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'.
Genome build of coordinate input. Ignored for HGVS/rsID.
Force this transcript for the classification, e.g. NM_000546.6
Force this gene for the classification, e.g. TP53
Annotate and classify one human genetic variant using GeneBe. Start here for any question about a variant (what is it, is it pathogenic/benign, how common is it). Returns the ACMG verdict with points and criteria, population frequency (gnomAD), predictor scores (REVEL, AlphaMissense, SpliceAI, ...), ClinVar status, transcript consequences, and links to the GeneBe page to cite. Research use only; not a diagnosis.
| Argument | Type | Description |
|---|---|---|
| genome | string | Genome build of coordinate input. Ignored for HGVS/rsID. |
| variant* | string | 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'. |
| transcript | any | Force this transcript for the classification, e.g. NM_000546.6 |
| gene_symbol | any | Force this gene for the classification, e.g. TP53 |
{
"type": "object",
"title": "annotate_variantArguments",
"required": [
"variant"
],
"properties": {
"genome": {
"enum": [
"hg19",
"hg38",
"t2t"
],
"type": "string",
"title": "Genome",
"default": "hg38",
"description": "Genome build of coordinate input. Ignored for HGVS/rsID."
},
"variant": {
"type": "string",
"title": "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'."
},
"transcript": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Transcript",
"default": null,
"description": "Force this transcript for the classification, e.g. NM_000546.6"
},
"gene_symbol": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Gene Symbol",
"default": null,
"description": "Force this gene for the classification, e.g. TP53"
}
}
}Convert a variant written in any notation into normalized hg38 genomic coordinates. Use when you only need the chr/pos/ref/alt of a variant (for example to translate HGVS or an rsID), without annotation. Does not classify the variant; use annotate_variant for that.
| Argument | Type | Description |
|---|---|---|
| variant* | string | HGVS (NM_007294.4:c.3756_3759del), rsID (rs429358), SPDI (NC_000007.14:11324573:C:T), 'chr-pos-ref-alt', or 'GENE p.Thr1700Ile'. |
| input_genome | string | Genome build of positional input (hg19 input is lifted to hg38). |
{
"type": "object",
"title": "convert_variantArguments",
"required": [
"variant"
],
"properties": {
"variant": {
"type": "string",
"title": "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'."
},
"input_genome": {
"enum": [
"hg19",
"hg38",
"t2t"
],
"type": "string",
"title": "Input Genome",
"default": "hg38",
"description": "Genome build of positional input (hg19 input is lifted to hg38)."
}
}
}Explain step by step why each classification criterion did or did not apply to a variant. Use after annotate_variant when the user asks "why was this classified that way?". Returns an ASCII rendering of the decision tree with the evaluated conditions. By default it explains the germline ACMG verdict that annotate_variant returns; the somatic trees 'oncogenicity' (2022) and 'acgs-uk-onco' (2025) can be requested explicitly. Research use only.
| Argument | Type | Description |
|---|---|---|
| tree | string | Decision tree: 'germline' (default), 'oncogenicity' or 'acgs-uk-onco'. |
| genome | string | Genome build of coordinate input. |
| variant* | string | The variant, in any notation accepted by annotate_variant. |
| version | string | Tree version: germline 2019 (default), oncogenicity 2022, acgs-uk-onco 2025. |
{
"type": "object",
"title": "explain_acmg_decision_pathArguments",
"required": [
"variant"
],
"properties": {
"tree": {
"type": "string",
"title": "Tree",
"default": "germline",
"description": "Decision tree: 'germline' (default), 'oncogenicity' or 'acgs-uk-onco'."
},
"genome": {
"enum": [
"hg19",
"hg38",
"t2t"
],
"type": "string",
"title": "Genome",
"default": "hg38",
"description": "Genome build of coordinate input."
},
"variant": {
"type": "string",
"title": "Variant",
"description": "The variant, in any notation accepted by annotate_variant."
},
"version": {
"type": "string",
"title": "Version",
"default": "2019",
"description": "Tree version: germline 2019 (default), oncogenicity 2022, acgs-uk-onco 2025."
}
}
}Look up a human gene: identifiers, location, MANE Select transcript, ClinGen gene-disease validity. Use for questions about a gene rather than a specific variant. Transcripts are listed with MANE Select first and capped; check total_transcripts.
| Argument | Type | Description |
|---|---|---|
| gene* | string | Gene symbol (BRCA1), alias, HGNC id (HGNC:1100), 'entrez:672' or Ensembl id (ENSG...). |
| include_transcripts | boolean | Also list the gene's transcripts. |
{
"type": "object",
"title": "get_geneArguments",
"required": [
"gene"
],
"properties": {
"gene": {
"type": "string",
"title": "Gene",
"description": "Gene symbol (BRCA1), alias, HGNC id (HGNC:1100), 'entrez:672' or Ensembl id (ENSG...)."
},
"include_transcripts": {
"type": "boolean",
"title": "Include Transcripts",
"default": true,
"description": "Also list the gene's transcripts."
}
}
}List a variant's predicted molecular consequences on every overlapping transcript. Returns per-transcript HGVS (c. and p.), consequence terms (e.g. missense_variant) and impact, most severe and MANE Select transcripts first. Lightweight: no frequencies or classification.
| Argument | Type | Description |
|---|---|---|
| genome | string | Genome build of coordinate input. |
| variant* | string | The variant, in any notation accepted by annotate_variant. |
{
"type": "object",
"title": "get_variant_effectsArguments",
"required": [
"variant"
],
"properties": {
"genome": {
"enum": [
"hg19",
"hg38",
"t2t"
],
"type": "string",
"title": "Genome",
"default": "hg38",
"description": "Genome build of coordinate input."
},
"variant": {
"type": "string",
"title": "Variant",
"description": "The variant, in any notation accepted by annotate_variant."
}
}
}Convert a genomic position, interval or variant between genome builds (hg19, hg38, t2t). Check `status`: RESOLVED means one result, AMBIGUOUS means several candidates, anything else means it could not be mapped (see errors). For variants, ref/alt are rebuilt against the target reference and warnings such as REF_MISMATCH may apply.
| Argument | Type | Description |
|---|---|---|
| query* | string | A position ('chr8:141310715'), an interval ('chr8:141310715-141310716') or a variant ('chr2-23423-A-C', HGVS, rsID). |
| to_genome* | string | Genome build to convert to. |
| from_genome* | string | Genome build of the input. |
{
"type": "object",
"title": "liftover_coordinateArguments",
"required": [
"query",
"from_genome",
"to_genome"
],
"properties": {
"query": {
"type": "string",
"title": "Query",
"description": "A position ('chr8:141310715'), an interval ('chr8:141310715-141310716') or a variant ('chr2-23423-A-C', HGVS, rsID)."
},
"to_genome": {
"enum": [
"hg19",
"hg38",
"t2t"
],
"type": "string",
"title": "To Genome",
"description": "Genome build to convert to."
},
"from_genome": {
"enum": [
"hg19",
"hg38",
"t2t"
],
"type": "string",
"title": "From Genome",
"description": "Genome build of the input."
}
}
}