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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: 11-5227003-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=5227003&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 5227003,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000335295.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"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.19G>A",
"hgvs_p": "p.Glu7Lys",
"transcript": "NM_000518.5",
"protein_id": "NP_000509.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 147,
"cds_start": 19,
"cds_end": null,
"cds_length": 444,
"cdna_start": 69,
"cdna_end": null,
"cdna_length": 628,
"mane_select": "ENST00000335295.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"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.19G>A",
"hgvs_p": "p.Glu7Lys",
"transcript": "ENST00000335295.4",
"protein_id": "ENSP00000333994.3",
"transcript_support_level": 1,
"aa_start": 7,
"aa_end": null,
"aa_length": 147,
"cds_start": 19,
"cds_end": null,
"cds_length": 444,
"cdna_start": 69,
"cdna_end": null,
"cdna_length": 628,
"mane_select": "NM_000518.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"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.19G>A",
"hgvs_p": "p.Glu7Lys",
"transcript": "ENST00000485743.1",
"protein_id": "ENSP00000496200.1",
"transcript_support_level": 1,
"aa_start": 7,
"aa_end": null,
"aa_length": 111,
"cds_start": 19,
"cds_end": null,
"cds_length": 336,
"cdna_start": 70,
"cdna_end": null,
"cdna_length": 680,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"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.19G>A",
"hgvs_p": "p.Glu7Lys",
"transcript": "ENST00000647020.1",
"protein_id": "ENSP00000494175.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 147,
"cds_start": 19,
"cds_end": null,
"cds_length": 444,
"cdna_start": 195,
"cdna_end": null,
"cdna_length": 754,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"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.19G>A",
"hgvs_p": "p.Glu7Lys",
"transcript": "ENST00000380315.2",
"protein_id": "ENSP00000369671.2",
"transcript_support_level": 5,
"aa_start": 7,
"aa_end": null,
"aa_length": 89,
"cds_start": 19,
"cds_end": null,
"cds_length": 272,
"cdna_start": 249,
"cdna_end": null,
"cdna_length": 502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.19G>A",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 609,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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+1275C>T",
"hgvs_p": null,
"transcript": "ENST00000759072.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.-180G>A",
"hgvs_p": null,
"transcript": "ENST00000475226.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 319,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HBB",
"gene_hgnc_id": 4827,
"dbsnp": "rs33930165",
"frequency_reference_population": 0.000736175,
"hom_count_reference_population": 7,
"allele_count_reference_population": 1186,
"gnomad_exomes_af": 0.000421609,
"gnomad_genomes_af": 0.00374834,
"gnomad_exomes_ac": 615,
"gnomad_genomes_ac": 571,
"gnomad_exomes_homalt": 6,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.014550089836120605,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.45,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2696,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.632,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM5,PP5_Very_Strong,BP4,BS2_Supporting",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 2,
"pathogenic_score": 12,
"criteria": [
"PM1",
"PM5",
"PP5_Very_Strong",
"BP4",
"BS2_Supporting"
],
"verdict": "Pathogenic",
"transcript": "ENST00000335295.4",
"gene_symbol": "HBB",
"hgnc_id": 4827,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.19G>A",
"hgvs_p": "p.Glu7Lys"
},
{
"score": 3,
"benign_score": 5,
"pathogenic_score": 8,
"criteria": [
"PP5_Very_Strong",
"BP4",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000759072.1",
"gene_symbol": "ENSG00000298932",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.265+1275C>T",
"hgvs_p": null
}
],
"clinvar_disease": " resistance to,8 conditions,9 conditions,Beta-thalassemia HBB/LCRB,Dominant beta-thalassemia,HBB-related disorder,HEMOGLOBIN C,Hb SS disease,Heinz body anemia,Hereditary persistence of fetal hemoglobin,Inborn genetic diseases,Inherited hemoglobinopathy,Malaria,Sickle cell-hemoglobin C disease,alpha Thalassemia,beta Thalassemia,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:27 LP:2 O:1",
"phenotype_combined": "Malaria, resistance to|not provided|HEMOGLOBIN C|Hb SS disease|beta Thalassemia|Inborn genetic diseases|Heinz body anemia|Beta-thalassemia HBB/LCRB|9 conditions|8 conditions|Hereditary persistence of fetal hemoglobin|Sickle cell-hemoglobin C disease|Hb SS disease;alpha Thalassemia;Heinz body anemia;Beta-thalassemia HBB/LCRB;Dominant beta-thalassemia|HBB-related disorder|Inherited hemoglobinopathy",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}