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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: 2-26458112-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=26458112&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 11,
"criteria": [
"BP4",
"BP6",
"BP7",
"BS1",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "OTOF",
"hgnc_id": 8515,
"hgvs_c": "c.5922G>A",
"hgvs_p": "p.Leu1974Leu",
"inheritance_mode": "AR,Unknown",
"pathogenic_score": 0,
"score": -11,
"transcript": "NM_001287489.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4,BP6,BP7,BS1,BS2",
"acmg_score": -11,
"allele_count_reference_population": 1204,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.18,
"chr": "2",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Autosomal recessive nonsyndromic hearing loss 9,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1 B:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.18000000715255737,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1230,
"aa_ref": "L",
"aa_start": 1207,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4838,
"cdna_start": 3929,
"cds_end": null,
"cds_length": 3693,
"cds_start": 3621,
"consequences": [
"synonymous_variant"
],
"exon_count": 29,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "NM_194323.3",
"gene_hgnc_id": 8515,
"gene_symbol": "OTOF",
"hgvs_c": "c.3621G>A",
"hgvs_p": "p.Leu1207Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": "ENST00000339598.8",
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_919304.1",
"strand": false,
"transcript": "NM_194323.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1230,
"aa_ref": "L",
"aa_start": 1207,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4838,
"cdna_start": 3929,
"cds_end": null,
"cds_length": 3693,
"cds_start": 3621,
"consequences": [
"synonymous_variant"
],
"exon_count": 29,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "ENST00000339598.8",
"gene_hgnc_id": 8515,
"gene_symbol": "OTOF",
"hgvs_c": "c.3621G>A",
"hgvs_p": "p.Leu1207Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": "NM_194323.3",
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000344521.3",
"strand": false,
"transcript": "ENST00000339598.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1997,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7214,
"cdna_start": null,
"cds_end": null,
"cds_length": 5994,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 47,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "NM_194248.3",
"gene_hgnc_id": 8515,
"gene_symbol": "OTOF",
"hgvs_c": "c.*126G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000272371.7",
"protein_coding": true,
"protein_id": "NP_919224.1",
"strand": false,
"transcript": "NM_194248.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1997,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7214,
"cdna_start": null,
"cds_end": null,
"cds_length": 5994,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 47,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000272371.7",
"gene_hgnc_id": 8515,
"gene_symbol": "OTOF",
"hgvs_c": "c.*126G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_194248.3",
"protein_coding": true,
"protein_id": "ENSP00000272371.2",
"strand": false,
"transcript": "ENST00000272371.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1250,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5108,
"cdna_start": null,
"cds_end": null,
"cds_length": 3753,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 29,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "ENST00000402415.8",
"gene_hgnc_id": 8515,
"gene_symbol": "OTOF",
"hgvs_c": "c.*126G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000383906.4",
"strand": false,
"transcript": "ENST00000402415.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1230,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4954,
"cdna_start": null,
"cds_end": null,
"cds_length": 3693,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 30,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "ENST00000338581.10",
"gene_hgnc_id": 8515,
"gene_symbol": "OTOF",
"hgvs_c": "c.*126G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000345137.6",
"strand": false,
"transcript": "ENST00000338581.10",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1997,
"aa_ref": "L",
"aa_start": 1974,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7016,
"cdna_start": 6107,
"cds_end": null,
"cds_length": 5994,
"cds_start": 5922,
"consequences": [
"synonymous_variant"
],
"exon_count": 46,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "NM_001287489.2",
"gene_hgnc_id": 8515,
"gene_symbol": "OTOF",
"hgvs_c": "c.5922G>A",
"hgvs_p": "p.Leu1974Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001274418.1",
"strand": false,
"transcript": "NM_001287489.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1997,
"aa_ref": "L",
"aa_start": 1974,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6937,
"cdna_start": 6029,
"cds_end": null,
"cds_length": 5994,
"cds_start": 5922,
"consequences": [
"synonymous_variant"
],
"exon_count": 46,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "ENST00000403946.7",
"gene_hgnc_id": 8515,
"gene_symbol": "OTOF",
"hgvs_c": "c.5922G>A",
"hgvs_p": "p.Leu1974Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000385255.3",
"strand": false,
"transcript": "ENST00000403946.7",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1307,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5190,
"cdna_start": null,
"cds_end": null,
"cds_length": 3924,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 29,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "NM_194322.3",
"gene_hgnc_id": 8515,
"gene_symbol": "OTOF",
"hgvs_c": "c.*126G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_919303.1",
"strand": false,
"transcript": "NM_194322.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1230,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5036,
"cdna_start": null,
"cds_end": null,
"cds_length": 3693,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 30,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "NM_004802.4",
"gene_hgnc_id": 8515,
"gene_symbol": "OTOF",
"hgvs_c": "c.*126G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_004793.2",
"strand": false,
"transcript": "NM_004802.4",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs73920281",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0007458831,
"gene_hgnc_id": 8515,
"gene_symbol": "OTOF",
"gnomad_exomes_ac": 578,
"gnomad_exomes_af": 0.000395383,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_ac": 626,
"gnomad_genomes_af": 0.00410977,
"gnomad_genomes_homalt": 4,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 9,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|Autosomal recessive nonsyndromic hearing loss 9|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.356,
"pos": 26458112,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001287489.2"
}
]
}