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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: 16-89707880-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=89707880&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 89707880,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004913.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1877G>A",
"hgvs_p": "p.Arg626Gln",
"transcript": "NM_004913.3",
"protein_id": "NP_004904.2",
"transcript_support_level": null,
"aa_start": 626,
"aa_end": null,
"aa_length": 631,
"cds_start": 1877,
"cds_end": null,
"cds_length": 1896,
"cdna_start": 1914,
"cdna_end": null,
"cdna_length": 2660,
"mane_select": "ENST00000389386.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1877G>A",
"hgvs_p": "p.Arg626Gln",
"transcript": "ENST00000389386.8",
"protein_id": "ENSP00000374037.3",
"transcript_support_level": 1,
"aa_start": 626,
"aa_end": null,
"aa_length": 631,
"cds_start": 1877,
"cds_end": null,
"cds_length": 1896,
"cdna_start": 1914,
"cdna_end": null,
"cdna_length": 2660,
"mane_select": "NM_004913.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1667G>A",
"hgvs_p": "p.Arg556Gln",
"transcript": "ENST00000561976.5",
"protein_id": "ENSP00000454244.1",
"transcript_support_level": 1,
"aa_start": 556,
"aa_end": null,
"aa_length": 561,
"cds_start": 1667,
"cds_end": null,
"cds_length": 1686,
"cdna_start": 2045,
"cdna_end": null,
"cdna_length": 2791,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.677G>A",
"hgvs_p": "p.Arg226Gln",
"transcript": "ENST00000565023.1",
"protein_id": "ENSP00000455792.1",
"transcript_support_level": 5,
"aa_start": 226,
"aa_end": null,
"aa_length": 231,
"cds_start": 677,
"cds_end": null,
"cds_length": 696,
"cdna_start": 679,
"cdna_end": null,
"cdna_length": 775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1919G>A",
"hgvs_p": "p.Arg640Gln",
"transcript": "XM_047434930.1",
"protein_id": "XP_047290886.1",
"transcript_support_level": null,
"aa_start": 640,
"aa_end": null,
"aa_length": 645,
"cds_start": 1919,
"cds_end": null,
"cds_length": 1938,
"cdna_start": 1956,
"cdna_end": null,
"cdna_length": 2702,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1916G>A",
"hgvs_p": "p.Arg639Gln",
"transcript": "XM_047434931.1",
"protein_id": "XP_047290887.1",
"transcript_support_level": null,
"aa_start": 639,
"aa_end": null,
"aa_length": 644,
"cds_start": 1916,
"cds_end": null,
"cds_length": 1935,
"cdna_start": 1953,
"cdna_end": null,
"cdna_length": 2699,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1880G>A",
"hgvs_p": "p.Arg627Gln",
"transcript": "XM_005256329.6",
"protein_id": "XP_005256386.1",
"transcript_support_level": null,
"aa_start": 627,
"aa_end": null,
"aa_length": 632,
"cds_start": 1880,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1917,
"cdna_end": null,
"cdna_length": 2663,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1877G>A",
"hgvs_p": "p.Arg626Gln",
"transcript": "XM_011523476.4",
"protein_id": "XP_011521778.1",
"transcript_support_level": null,
"aa_start": 626,
"aa_end": null,
"aa_length": 631,
"cds_start": 1877,
"cds_end": null,
"cds_length": 1896,
"cdna_start": 1914,
"cdna_end": null,
"cdna_length": 2660,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1874G>A",
"hgvs_p": "p.Arg625Gln",
"transcript": "XM_047434932.1",
"protein_id": "XP_047290888.1",
"transcript_support_level": null,
"aa_start": 625,
"aa_end": null,
"aa_length": 630,
"cds_start": 1874,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1911,
"cdna_end": null,
"cdna_length": 2657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1817G>A",
"hgvs_p": "p.Arg606Gln",
"transcript": "XM_047434933.1",
"protein_id": "XP_047290889.1",
"transcript_support_level": null,
"aa_start": 606,
"aa_end": null,
"aa_length": 611,
"cds_start": 1817,
"cds_end": null,
"cds_length": 1836,
"cdna_start": 1821,
"cdna_end": null,
"cdna_length": 2567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1814G>A",
"hgvs_p": "p.Arg605Gln",
"transcript": "XM_047434934.1",
"protein_id": "XP_047290890.1",
"transcript_support_level": null,
"aa_start": 605,
"aa_end": null,
"aa_length": 610,
"cds_start": 1814,
"cds_end": null,
"cds_length": 1833,
"cdna_start": 1815,
"cdna_end": null,
"cdna_length": 2561,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1814G>A",
"hgvs_p": "p.Arg605Gln",
"transcript": "XM_047434935.1",
"protein_id": "XP_047290891.1",
"transcript_support_level": null,
"aa_start": 605,
"aa_end": null,
"aa_length": 610,
"cds_start": 1814,
"cds_end": null,
"cds_length": 1833,
"cdna_start": 1851,
"cdna_end": null,
"cdna_length": 2597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1772G>A",
"hgvs_p": "p.Arg591Gln",
"transcript": "XM_047434936.1",
"protein_id": "XP_047290892.1",
"transcript_support_level": null,
"aa_start": 591,
"aa_end": null,
"aa_length": 596,
"cds_start": 1772,
"cds_end": null,
"cds_length": 1791,
"cdna_start": 1809,
"cdna_end": null,
"cdna_length": 2555,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1709G>A",
"hgvs_p": "p.Arg570Gln",
"transcript": "XM_047434937.1",
"protein_id": "XP_047290893.1",
"transcript_support_level": null,
"aa_start": 570,
"aa_end": null,
"aa_length": 575,
"cds_start": 1709,
"cds_end": null,
"cds_length": 1728,
"cdna_start": 1999,
"cdna_end": null,
"cdna_length": 2745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"dbsnp": "rs61747704",
"frequency_reference_population": 0.00011158763,
"hom_count_reference_population": 0,
"allele_count_reference_population": 180,
"gnomad_exomes_af": 0.0000650342,
"gnomad_genomes_af": 0.000558065,
"gnomad_exomes_ac": 95,
"gnomad_genomes_ac": 85,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005753964185714722,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.03,
"revel_prediction": "Benign",
"alphamissense_score": 0.0636,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.227,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_004913.3",
"gene_symbol": "VPS9D1",
"hgnc_id": 13526,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1877G>A",
"hgvs_p": "p.Arg626Gln"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}