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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: 11-5227002-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=5227002&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 5227002,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000518.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBB",
"gene_hgnc_id": 4827,
"hgvs_c": "c.20A>T",
"hgvs_p": "p.Glu7Val",
"transcript": "NM_000518.5",
"protein_id": "NP_000509.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 147,
"cds_start": 20,
"cds_end": null,
"cds_length": 444,
"cdna_start": 70,
"cdna_end": null,
"cdna_length": 628,
"mane_select": "ENST00000335295.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000518.5"
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBB",
"gene_hgnc_id": 4827,
"hgvs_c": "c.20A>T",
"hgvs_p": "p.Glu7Val",
"transcript": "ENST00000335295.4",
"protein_id": "ENSP00000333994.3",
"transcript_support_level": 1,
"aa_start": 7,
"aa_end": null,
"aa_length": 147,
"cds_start": 20,
"cds_end": null,
"cds_length": 444,
"cdna_start": 70,
"cdna_end": null,
"cdna_length": 628,
"mane_select": "NM_000518.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000335295.4"
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBB",
"gene_hgnc_id": 4827,
"hgvs_c": "c.20A>T",
"hgvs_p": "p.Glu7Val",
"transcript": "ENST00000485743.1",
"protein_id": "ENSP00000496200.1",
"transcript_support_level": 1,
"aa_start": 7,
"aa_end": null,
"aa_length": 111,
"cds_start": 20,
"cds_end": null,
"cds_length": 336,
"cdna_start": 71,
"cdna_end": null,
"cdna_length": 680,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000485743.1"
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBB",
"gene_hgnc_id": 4827,
"hgvs_c": "c.20A>T",
"hgvs_p": "p.Glu7Val",
"transcript": "ENST00000647020.1",
"protein_id": "ENSP00000494175.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 147,
"cds_start": 20,
"cds_end": null,
"cds_length": 444,
"cdna_start": 196,
"cdna_end": null,
"cdna_length": 754,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000647020.1"
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBB",
"gene_hgnc_id": 4827,
"hgvs_c": "c.20A>T",
"hgvs_p": "p.Glu7Val",
"transcript": "ENST00000883533.1",
"protein_id": "ENSP00000553592.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 147,
"cds_start": 20,
"cds_end": null,
"cds_length": 444,
"cdna_start": 144,
"cdna_end": null,
"cdna_length": 702,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883533.1"
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBB",
"gene_hgnc_id": 4827,
"hgvs_c": "c.20A>T",
"hgvs_p": "p.Glu7Val",
"transcript": "ENST00000380315.2",
"protein_id": "ENSP00000369671.2",
"transcript_support_level": 5,
"aa_start": 7,
"aa_end": null,
"aa_length": 89,
"cds_start": 20,
"cds_end": null,
"cds_length": 272,
"cdna_start": 250,
"cdna_end": null,
"cdna_length": 502,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000380315.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBB",
"gene_hgnc_id": 4827,
"hgvs_c": "n.20A>T",
"hgvs_p": null,
"transcript": "ENST00000633227.1",
"protein_id": "ENSP00000488004.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 609,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000633227.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000298932",
"gene_hgnc_id": null,
"hgvs_c": "n.265+1274T>A",
"hgvs_p": null,
"transcript": "ENST00000759072.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 336,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000759072.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBB",
"gene_hgnc_id": 4827,
"hgvs_c": "n.-179A>T",
"hgvs_p": null,
"transcript": "ENST00000475226.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 319,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000475226.1"
}
],
"gene_symbol": "HBB",
"gene_hgnc_id": 4827,
"dbsnp": "rs334",
"frequency_reference_population": 0.0026523452,
"hom_count_reference_population": 40,
"allele_count_reference_population": 4272,
"gnomad_exomes_af": 0.00160112,
"gnomad_genomes_af": 0.0127188,
"gnomad_exomes_ac": 2335,
"gnomad_genomes_ac": 1937,
"gnomad_exomes_homalt": 31,
"gnomad_genomes_homalt": 9,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.007841616868972778,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.535,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2229,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 0.69,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PS3,PM1,PM5,PP5_Very_Strong,BP4,BA1",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 9,
"pathogenic_score": 16,
"criteria": [
"PS3",
"PM1",
"PM5",
"PP5_Very_Strong",
"BP4",
"BA1"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_000518.5",
"gene_symbol": "HBB",
"hgnc_id": 4827,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.20A>T",
"hgvs_p": "p.Glu7Val"
},
{
"score": 3,
"benign_score": 9,
"pathogenic_score": 12,
"criteria": [
"PS3",
"PP5_Very_Strong",
"BP4",
"BA1"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000759072.1",
"gene_symbol": "ENSG00000298932",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.265+1274T>A",
"hgvs_p": null
}
],
"clinvar_disease": " resistance to, susceptibility to,6 conditions,8 conditions,9 conditions,Beta-thalassemia HBB/LCRB,Dominant beta-thalassemia,Fetal hemoglobin quantitative trait locus 1,HBB-related disorder,HEMOGLOBIN S,Hb SS disease,Heinz body anemia,Hereditary persistence of fetal hemoglobin,Inborn genetic diseases,Malaria,See cases,Sickle cell disease and related diseases,Sickle cell-hemoglobin C disease,alpha Thalassemia,beta Thalassemia,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:47 O:4",
"phenotype_combined": "HEMOGLOBIN S|Hb SS disease|Malaria, resistance to|Inborn genetic diseases|Sickle cell disease and related diseases|not provided|beta Thalassemia|6 conditions|See cases|Beta-thalassemia HBB/LCRB|9 conditions|HBB-related disorder|Fetal hemoglobin quantitative trait locus 1|Sickle cell-hemoglobin C disease|Malaria, susceptibility to|8 conditions|Hb SS disease;alpha Thalassemia;Heinz body anemia;Beta-thalassemia HBB/LCRB;Dominant beta-thalassemia|Hereditary persistence of fetal hemoglobin",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}