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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 17-75830410-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=75830410&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "UNC13D",
"hgnc_id": 23147,
"hgvs_c": "c.2782C>T",
"hgvs_p": "p.Arg928Cys",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_199242.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 32119,
"alphamissense_prediction": null,
"alphamissense_score": 0.0986,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.23,
"chr": "17",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "Autoinflammatory syndrome,Familial hemophagocytic lymphohistiocytosis 3,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:5 B:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.008826911449432373,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1090,
"aa_ref": "R",
"aa_start": 928,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4080,
"cdna_start": 2849,
"cds_end": null,
"cds_length": 3273,
"cds_start": 2782,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "NM_199242.3",
"gene_hgnc_id": 23147,
"gene_symbol": "UNC13D",
"hgvs_c": "c.2782C>T",
"hgvs_p": "p.Arg928Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000207549.9",
"protein_coding": true,
"protein_id": "NP_954712.1",
"strand": false,
"transcript": "NM_199242.3",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1090,
"aa_ref": "R",
"aa_start": 928,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4080,
"cdna_start": 2849,
"cds_end": null,
"cds_length": 3273,
"cds_start": 2782,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "ENST00000207549.9",
"gene_hgnc_id": 23147,
"gene_symbol": "UNC13D",
"hgvs_c": "c.2782C>T",
"hgvs_p": "p.Arg928Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_199242.3",
"protein_coding": true,
"protein_id": "ENSP00000207549.3",
"strand": false,
"transcript": "ENST00000207549.9",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1142,
"aa_ref": "R",
"aa_start": 928,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3648,
"cdna_start": 2795,
"cds_end": null,
"cds_length": 3429,
"cds_start": 2782,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "ENST00000412096.6",
"gene_hgnc_id": 23147,
"gene_symbol": "UNC13D",
"hgvs_c": "c.2782C>T",
"hgvs_p": "p.Arg928Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000388093.1",
"strand": false,
"transcript": "ENST00000412096.6",
"transcript_support_level": 2
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1090,
"aa_ref": "R",
"aa_start": 928,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4084,
"cdna_start": 2853,
"cds_end": null,
"cds_length": 3273,
"cds_start": 2782,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "ENST00000868100.1",
"gene_hgnc_id": 23147,
"gene_symbol": "UNC13D",
"hgvs_c": "c.2782C>T",
"hgvs_p": "p.Arg928Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538159.1",
"strand": false,
"transcript": "ENST00000868100.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1090,
"aa_ref": "R",
"aa_start": 928,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4078,
"cdna_start": 2865,
"cds_end": null,
"cds_length": 3273,
"cds_start": 2782,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "ENST00000868101.1",
"gene_hgnc_id": 23147,
"gene_symbol": "UNC13D",
"hgvs_c": "c.2782C>T",
"hgvs_p": "p.Arg928Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538160.1",
"strand": false,
"transcript": "ENST00000868101.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1073,
"aa_ref": "R",
"aa_start": 911,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4057,
"cdna_start": 2826,
"cds_end": null,
"cds_length": 3222,
"cds_start": 2731,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "ENST00000965711.1",
"gene_hgnc_id": 23147,
"gene_symbol": "UNC13D",
"hgvs_c": "c.2731C>T",
"hgvs_p": "p.Arg911Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635770.1",
"strand": false,
"transcript": "ENST00000965711.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1059,
"aa_ref": "R",
"aa_start": 897,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4301,
"cdna_start": 3070,
"cds_end": null,
"cds_length": 3180,
"cds_start": 2689,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000965712.1",
"gene_hgnc_id": 23147,
"gene_symbol": "UNC13D",
"hgvs_c": "c.2689C>T",
"hgvs_p": "p.Arg897Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635771.1",
"strand": false,
"transcript": "ENST00000965712.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 712,
"aa_ref": "R",
"aa_start": 550,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2740,
"cdna_start": 1648,
"cds_end": null,
"cds_length": 2139,
"cds_start": 1648,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000699510.1",
"gene_hgnc_id": 23147,
"gene_symbol": "UNC13D",
"hgvs_c": "c.1648C>T",
"hgvs_p": "p.Arg550Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000514405.1",
"strand": false,
"transcript": "ENST00000699510.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 403,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000586519.1",
"gene_hgnc_id": 23147,
"gene_symbol": "UNC13D",
"hgvs_c": "n.28C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000466149.1",
"strand": false,
"transcript": "ENST00000586519.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 695,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000590856.1",
"gene_hgnc_id": 23147,
"gene_symbol": "UNC13D",
"hgvs_c": "n.157C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000590856.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs35037984",
"effect": "missense_variant",
"frequency_reference_population": 0.020222224,
"gene_hgnc_id": 23147,
"gene_symbol": "UNC13D",
"gnomad_exomes_ac": 29491,
"gnomad_exomes_af": 0.0205364,
"gnomad_exomes_homalt": 354,
"gnomad_genomes_ac": 2628,
"gnomad_genomes_af": 0.0172595,
"gnomad_genomes_homalt": 36,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 390,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "not specified|Familial hemophagocytic lymphohistiocytosis 3|Autoinflammatory syndrome|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.919,
"pos": 75830410,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.4,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_199242.3"
}
]
}