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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: 16-2498261-AT-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2498261&ref=AT&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 2498261,
"ref": "AT",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "ENST00000646147.1",
"consequences": [
{
"aa_ref": "H",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "c.1008delT",
"hgvs_p": "p.His336fs",
"transcript": "NM_001199107.2",
"protein_id": "NP_001186036.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 559,
"cds_start": 1008,
"cds_end": null,
"cds_length": 1680,
"cdna_start": 1167,
"cdna_end": null,
"cdna_length": 6611,
"mane_select": "ENST00000646147.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "c.1008delT",
"hgvs_p": "p.His336fs",
"transcript": "ENST00000646147.1",
"protein_id": "ENSP00000494678.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 559,
"cds_start": 1008,
"cds_end": null,
"cds_length": 1680,
"cdna_start": 1167,
"cdna_end": null,
"cdna_length": 6611,
"mane_select": "NM_001199107.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "c.990delT",
"hgvs_p": "p.His330fs",
"transcript": "ENST00000567020.7",
"protein_id": "ENSP00000454408.1",
"transcript_support_level": 1,
"aa_start": 330,
"aa_end": null,
"aa_length": 553,
"cds_start": 990,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1225,
"cdna_end": null,
"cdna_length": 10610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000260272",
"gene_hgnc_id": null,
"hgvs_c": "c.965+1149delT",
"hgvs_p": null,
"transcript": "ENST00000564543.1",
"protein_id": "ENSP00000455547.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 376,
"cds_start": -4,
"cds_end": null,
"cds_length": 1131,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1944,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "c.990delT",
"hgvs_p": "p.His330fs",
"transcript": "NM_020705.3",
"protein_id": "NP_065756.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 553,
"cds_start": 990,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1149,
"cdna_end": null,
"cdna_length": 6593,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "c.990delT",
"hgvs_p": "p.His330fs",
"transcript": "ENST00000627285.1",
"protein_id": "ENSP00000486121.1",
"transcript_support_level": 5,
"aa_start": 330,
"aa_end": null,
"aa_length": 553,
"cds_start": 990,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1215,
"cdna_end": null,
"cdna_length": 4382,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "c.990delT",
"hgvs_p": "p.His330fs",
"transcript": "ENST00000643767.1",
"protein_id": "ENSP00000494145.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 464,
"cds_start": 990,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 1155,
"cdna_end": null,
"cdna_length": 1560,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "c.1008delT",
"hgvs_p": "p.His336fs",
"transcript": "ENST00000562105.2",
"protein_id": "ENSP00000457896.2",
"transcript_support_level": 3,
"aa_start": 336,
"aa_end": null,
"aa_length": 454,
"cds_start": 1008,
"cds_end": null,
"cds_length": 1367,
"cdna_start": 1191,
"cdna_end": null,
"cdna_length": 1550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "c.1008delT",
"hgvs_p": "p.His336fs",
"transcript": "XM_017023493.2",
"protein_id": "XP_016878982.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 559,
"cds_start": 1008,
"cds_end": null,
"cds_length": 1680,
"cdna_start": 1167,
"cdna_end": null,
"cdna_length": 5874,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "c.1008delT",
"hgvs_p": "p.His336fs",
"transcript": "XM_047434388.1",
"protein_id": "XP_047290344.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 559,
"cds_start": 1008,
"cds_end": null,
"cds_length": 1680,
"cdna_start": 1191,
"cdna_end": null,
"cdna_length": 6635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "c.990delT",
"hgvs_p": "p.His330fs",
"transcript": "XM_017023494.2",
"protein_id": "XP_016878983.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 553,
"cds_start": 990,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1173,
"cdna_end": null,
"cdna_length": 6617,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "c.990delT",
"hgvs_p": "p.His330fs",
"transcript": "XM_017023495.2",
"protein_id": "XP_016878984.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 553,
"cds_start": 990,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1149,
"cdna_end": null,
"cdna_length": 5856,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "n.990delT",
"hgvs_p": null,
"transcript": "ENST00000569874.2",
"protein_id": "ENSP00000455005.2",
"transcript_support_level": 5,
"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": 3061,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "n.986delT",
"hgvs_p": null,
"transcript": "ENST00000630263.2",
"protein_id": "ENSP00000486835.1",
"transcript_support_level": 5,
"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": 4180,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"hgvs_c": "n.-61delT",
"hgvs_p": null,
"transcript": "ENST00000564879.2",
"protein_id": "ENSP00000457266.2",
"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": 5324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TBC1D24",
"gene_hgnc_id": 29203,
"dbsnp": "rs398122967",
"frequency_reference_population": 0.00006765505,
"hom_count_reference_population": 0,
"allele_count_reference_population": 109,
"gnomad_exomes_af": 0.0000692264,
"gnomad_genomes_af": 0.0000525852,
"gnomad_exomes_ac": 101,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": -1.056,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000646147.1",
"gene_symbol": "TBC1D24",
"hgnc_id": 29203,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1008delT",
"hgvs_p": "p.His336fs"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000564543.1",
"gene_symbol": "ENSG00000260272",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.965+1149delT",
"hgvs_p": null
}
],
"clinvar_disease": " 1, 16, member 24,Autosomal dominant nonsyndromic hearing loss 65,Caused by mutation in the TBC1 domain family,DOORS syndrome,Developmental and epileptic encephalopathy,Inborn genetic diseases,TBC1D24-related disorder,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:11 O:1",
"phenotype_combined": "DOORS syndrome|not provided|Autosomal dominant nonsyndromic hearing loss 65|Developmental and epileptic encephalopathy, 1;Caused by mutation in the TBC1 domain family, member 24;Autosomal dominant nonsyndromic hearing loss 65|Inborn genetic diseases|TBC1D24-related disorder|Developmental and epileptic encephalopathy, 16",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}