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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: 9-136523964-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=136523964&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 21,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "NOTCH1",
"hgnc_id": 7881,
"hgvs_c": "c.156C>T",
"hgvs_p": "p.Phe52Phe",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -21,
"transcript": "NM_017617.5",
"verdict": "Benign"
},
{
"benign_score": 16,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC124902310",
"hgnc_id": null,
"hgvs_c": "n.623+531G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -16,
"transcript": "XR_007061865.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_score": -21,
"allele_count_reference_population": 465,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.75,
"chr": "9",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "Adams-Oliver syndrome 5,Aortic valve disease 1,Familial thoracic aortic aneurysm and aortic dissection,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.75,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2555,
"aa_ref": "F",
"aa_start": 52,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9568,
"cdna_start": 418,
"cds_end": null,
"cds_length": 7668,
"cds_start": 156,
"consequences": [
"synonymous_variant"
],
"exon_count": 34,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_017617.5",
"gene_hgnc_id": 7881,
"gene_symbol": "NOTCH1",
"hgvs_c": "c.156C>T",
"hgvs_p": "p.Phe52Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000651671.1",
"protein_coding": true,
"protein_id": "NP_060087.3",
"strand": false,
"transcript": "NM_017617.5",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2555,
"aa_ref": "F",
"aa_start": 52,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9568,
"cdna_start": 418,
"cds_end": null,
"cds_length": 7668,
"cds_start": 156,
"consequences": [
"synonymous_variant"
],
"exon_count": 34,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000651671.1",
"gene_hgnc_id": 7881,
"gene_symbol": "NOTCH1",
"hgvs_c": "c.156C>T",
"hgvs_p": "p.Phe52Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_017617.5",
"protein_coding": true,
"protein_id": "ENSP00000498587.1",
"strand": false,
"transcript": "ENST00000651671.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2518,
"aa_ref": "F",
"aa_start": 52,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9249,
"cdna_start": 221,
"cds_end": null,
"cds_length": 7557,
"cds_start": 156,
"consequences": [
"synonymous_variant"
],
"exon_count": 34,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000927794.1",
"gene_hgnc_id": 7881,
"gene_symbol": "NOTCH1",
"hgvs_c": "c.156C>T",
"hgvs_p": "p.Phe52Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000597853.1",
"strand": false,
"transcript": "ENST00000927794.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2517,
"aa_ref": "F",
"aa_start": 52,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9379,
"cdna_start": 367,
"cds_end": null,
"cds_length": 7554,
"cds_start": 156,
"consequences": [
"synonymous_variant"
],
"exon_count": 33,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000680133.1",
"gene_hgnc_id": 7881,
"gene_symbol": "NOTCH1",
"hgvs_c": "c.156C>T",
"hgvs_p": "p.Phe52Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000505319.1",
"strand": false,
"transcript": "ENST00000680133.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2517,
"aa_ref": "F",
"aa_start": 52,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9454,
"cdna_start": 418,
"cds_end": null,
"cds_length": 7554,
"cds_start": 156,
"consequences": [
"synonymous_variant"
],
"exon_count": 33,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000680668.1",
"gene_hgnc_id": 7881,
"gene_symbol": "NOTCH1",
"hgvs_c": "c.156C>T",
"hgvs_p": "p.Phe52Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000506336.1",
"strand": false,
"transcript": "ENST00000680668.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2515,
"aa_ref": "F",
"aa_start": 52,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9448,
"cdna_start": 418,
"cds_end": null,
"cds_length": 7548,
"cds_start": 156,
"consequences": [
"synonymous_variant"
],
"exon_count": 34,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000680218.1",
"gene_hgnc_id": 7881,
"gene_symbol": "NOTCH1",
"hgvs_c": "c.156C>T",
"hgvs_p": "p.Phe52Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000505339.1",
"strand": false,
"transcript": "ENST00000680218.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2314,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8598,
"cdna_start": null,
"cds_end": null,
"cds_length": 6945,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011518717.3",
"gene_hgnc_id": 7881,
"gene_symbol": "NOTCH1",
"hgvs_c": "c.20-4399C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011517019.2",
"strand": false,
"transcript": "XM_011518717.3",
"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": 9855,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 34,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000679595.1",
"gene_hgnc_id": 7881,
"gene_symbol": "NOTCH1",
"hgvs_c": "n.156C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000506241.1",
"strand": false,
"transcript": "ENST00000679595.1",
"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": 9525,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 34,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000680924.1",
"gene_hgnc_id": 7881,
"gene_symbol": "NOTCH1",
"hgvs_c": "n.156C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000506031.1",
"strand": false,
"transcript": "ENST00000680924.1",
"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": 9649,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 35,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000681135.1",
"gene_hgnc_id": 7881,
"gene_symbol": "NOTCH1",
"hgvs_c": "n.156C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000506636.1",
"strand": false,
"transcript": "ENST00000681135.1",
"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": 8966,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 32,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000681454.1",
"gene_hgnc_id": 7881,
"gene_symbol": "NOTCH1",
"hgvs_c": "n.141-4399C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000505763.1",
"strand": false,
"transcript": "ENST00000681454.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1103,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007061865.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC124902310",
"hgvs_c": "n.623+531G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007061865.1",
"transcript_support_level": null
},
{
"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": 799,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000491649.2",
"gene_hgnc_id": 7881,
"gene_symbol": "NOTCH1",
"hgvs_c": "n.-66C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000491649.2",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs536299678",
"effect": "synonymous_variant",
"frequency_reference_population": 0.00029880824,
"gene_hgnc_id": 7881,
"gene_symbol": "NOTCH1",
"gnomad_exomes_ac": 434,
"gnomad_exomes_af": 0.000309143,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_ac": 31,
"gnomad_genomes_af": 0.000203543,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 3,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "Adams-Oliver syndrome 5|Familial thoracic aortic aneurysm and aortic dissection|Aortic valve disease 1|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -1.812,
"pos": 136523964,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.05000000074505806,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.05,
"transcript": "NM_017617.5"
}
]
}