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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: 12-80339228-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=80339228&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "OTOGL",
"hgnc_id": 26901,
"hgvs_c": "c.5014C>T",
"hgvs_p": "p.Arg1672*",
"inheritance_mode": "AR",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_173591.7",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 99,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.29,
"chr": "12",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Autosomal recessive nonsyndromic hearing loss 84B,Rare genetic deafness,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.28999999165534973,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2353,
"aa_ref": "R",
"aa_start": 1672,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9982,
"cdna_start": 5102,
"cds_end": null,
"cds_length": 7062,
"cds_start": 5014,
"consequences": [
"stop_gained"
],
"exon_count": 59,
"exon_rank": 43,
"exon_rank_end": null,
"feature": "NM_001378609.3",
"gene_hgnc_id": 26901,
"gene_symbol": "OTOGL",
"hgvs_c": "c.5014C>T",
"hgvs_p": "p.Arg1672*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000547103.7",
"protein_coding": true,
"protein_id": "NP_001365538.2",
"strand": true,
"transcript": "NM_001378609.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2353,
"aa_ref": "R",
"aa_start": 1672,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9982,
"cdna_start": 5102,
"cds_end": null,
"cds_length": 7062,
"cds_start": 5014,
"consequences": [
"stop_gained"
],
"exon_count": 59,
"exon_rank": 43,
"exon_rank_end": null,
"feature": "ENST00000547103.7",
"gene_hgnc_id": 26901,
"gene_symbol": "OTOGL",
"hgvs_c": "c.5014C>T",
"hgvs_p": "p.Arg1672*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001378609.3",
"protein_coding": true,
"protein_id": "ENSP00000447211.2",
"strand": true,
"transcript": "ENST00000547103.7",
"transcript_support_level": 5
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2353,
"aa_ref": "R",
"aa_start": 1672,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10554,
"cdna_start": 5674,
"cds_end": null,
"cds_length": 7062,
"cds_start": 5014,
"consequences": [
"stop_gained"
],
"exon_count": 62,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "NM_001378610.3",
"gene_hgnc_id": 26901,
"gene_symbol": "OTOGL",
"hgvs_c": "c.5014C>T",
"hgvs_p": "p.Arg1672*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001365539.2",
"strand": true,
"transcript": "NM_001378610.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2353,
"aa_ref": "R",
"aa_start": 1672,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9972,
"cdna_start": 5092,
"cds_end": null,
"cds_length": 7062,
"cds_start": 5014,
"consequences": [
"stop_gained"
],
"exon_count": 59,
"exon_rank": 43,
"exon_rank_end": null,
"feature": "NM_173591.7",
"gene_hgnc_id": 26901,
"gene_symbol": "OTOGL",
"hgvs_c": "c.5014C>T",
"hgvs_p": "p.Arg1672*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_775862.4",
"strand": true,
"transcript": "NM_173591.7",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2308,
"aa_ref": "R",
"aa_start": 1627,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10859,
"cdna_start": 5979,
"cds_end": null,
"cds_length": 6927,
"cds_start": 4879,
"consequences": [
"stop_gained"
],
"exon_count": 63,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "NM_001368062.3",
"gene_hgnc_id": 26901,
"gene_symbol": "OTOGL",
"hgvs_c": "c.4879C>T",
"hgvs_p": "p.Arg1627*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001354991.2",
"strand": true,
"transcript": "NM_001368062.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2308,
"aa_ref": "R",
"aa_start": 1627,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9939,
"cdna_start": 5979,
"cds_end": null,
"cds_length": 6927,
"cds_start": 4879,
"consequences": [
"stop_gained"
],
"exon_count": 63,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000646859.1",
"gene_hgnc_id": 26901,
"gene_symbol": "OTOGL",
"hgvs_c": "c.4879C>T",
"hgvs_p": "p.Arg1627*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000496036.1",
"strand": true,
"transcript": "ENST00000646859.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 751,
"aa_ref": "R",
"aa_start": 105,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3289,
"cdna_start": 315,
"cds_end": null,
"cds_length": 2256,
"cds_start": 313,
"consequences": [
"stop_gained"
],
"exon_count": 18,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000298820.7",
"gene_hgnc_id": 26901,
"gene_symbol": "OTOGL",
"hgvs_c": "c.313C>T",
"hgvs_p": "p.Arg105*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000298820.3",
"strand": true,
"transcript": "ENST00000298820.7",
"transcript_support_level": 5
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2361,
"aa_ref": "R",
"aa_start": 1680,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10674,
"cdna_start": 5794,
"cds_end": null,
"cds_length": 7086,
"cds_start": 5038,
"consequences": [
"stop_gained"
],
"exon_count": 62,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "XM_005268802.4",
"gene_hgnc_id": 26901,
"gene_symbol": "OTOGL",
"hgvs_c": "c.5038C>T",
"hgvs_p": "p.Arg1680*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005268859.1",
"strand": true,
"transcript": "XM_005268802.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2326,
"aa_ref": "R",
"aa_start": 1645,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9869,
"cdna_start": 4989,
"cds_end": null,
"cds_length": 6981,
"cds_start": 4933,
"consequences": [
"stop_gained"
],
"exon_count": 56,
"exon_rank": 40,
"exon_rank_end": null,
"feature": "XM_011538193.2",
"gene_hgnc_id": 26901,
"gene_symbol": "OTOGL",
"hgvs_c": "c.4933C>T",
"hgvs_p": "p.Arg1645*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011536495.2",
"strand": true,
"transcript": "XM_011538193.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2310,
"aa_ref": "R",
"aa_start": 1629,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9880,
"cdna_start": 5000,
"cds_end": null,
"cds_length": 6933,
"cds_start": 4885,
"consequences": [
"stop_gained"
],
"exon_count": 56,
"exon_rank": 40,
"exon_rank_end": null,
"feature": "XM_011538192.3",
"gene_hgnc_id": 26901,
"gene_symbol": "OTOGL",
"hgvs_c": "c.4885C>T",
"hgvs_p": "p.Arg1629*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011536494.1",
"strand": true,
"transcript": "XM_011538192.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs759174628",
"effect": "stop_gained",
"frequency_reference_population": 0.00006178881,
"gene_hgnc_id": 26901,
"gene_symbol": "OTOGL",
"gnomad_exomes_ac": 98,
"gnomad_exomes_af": 0.0000674715,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000667708,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Rare genetic deafness|not provided|Autosomal recessive nonsyndromic hearing loss 84B",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.885,
"pos": 80339228,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.029999999329447746,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.03,
"transcript": "NM_173591.7"
}
]
}