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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: 2-26460998-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=26460998&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 26460998,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000272371.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOF",
"gene_hgnc_id": 8515,
"hgvs_c": "c.5566C>T",
"hgvs_p": "p.Arg1856Trp",
"transcript": "NM_194248.3",
"protein_id": "NP_919224.1",
"transcript_support_level": null,
"aa_start": 1856,
"aa_end": null,
"aa_length": 1997,
"cds_start": 5566,
"cds_end": null,
"cds_length": 5994,
"cdna_start": 5751,
"cdna_end": null,
"cdna_length": 7214,
"mane_select": "ENST00000272371.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOF",
"gene_hgnc_id": 8515,
"hgvs_c": "c.5566C>T",
"hgvs_p": "p.Arg1856Trp",
"transcript": "ENST00000272371.7",
"protein_id": "ENSP00000272371.2",
"transcript_support_level": 1,
"aa_start": 1856,
"aa_end": null,
"aa_length": 1997,
"cds_start": 5566,
"cds_end": null,
"cds_length": 5994,
"cdna_start": 5751,
"cdna_end": null,
"cdna_length": 7214,
"mane_select": "NM_194248.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOF",
"gene_hgnc_id": 8515,
"hgvs_c": "c.3265C>T",
"hgvs_p": "p.Arg1089Trp",
"transcript": "NM_194323.3",
"protein_id": "NP_919304.1",
"transcript_support_level": null,
"aa_start": 1089,
"aa_end": null,
"aa_length": 1230,
"cds_start": 3265,
"cds_end": null,
"cds_length": 3693,
"cdna_start": 3573,
"cdna_end": null,
"cdna_length": 4838,
"mane_select": null,
"mane_plus": "ENST00000339598.8",
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOF",
"gene_hgnc_id": 8515,
"hgvs_c": "c.3265C>T",
"hgvs_p": "p.Arg1089Trp",
"transcript": "ENST00000339598.8",
"protein_id": "ENSP00000344521.3",
"transcript_support_level": 1,
"aa_start": 1089,
"aa_end": null,
"aa_length": 1230,
"cds_start": 3265,
"cds_end": null,
"cds_length": 3693,
"cdna_start": 3573,
"cdna_end": null,
"cdna_length": 4838,
"mane_select": null,
"mane_plus": "NM_194323.3",
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOF",
"gene_hgnc_id": 8515,
"hgvs_c": "c.3325C>T",
"hgvs_p": "p.Arg1109Trp",
"transcript": "ENST00000402415.8",
"protein_id": "ENSP00000383906.4",
"transcript_support_level": 1,
"aa_start": 1109,
"aa_end": null,
"aa_length": 1250,
"cds_start": 3325,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 3645,
"cdna_end": null,
"cdna_length": 5108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOF",
"gene_hgnc_id": 8515,
"hgvs_c": "c.3265C>T",
"hgvs_p": "p.Arg1089Trp",
"transcript": "ENST00000338581.10",
"protein_id": "ENSP00000345137.6",
"transcript_support_level": 1,
"aa_start": 1089,
"aa_end": null,
"aa_length": 1230,
"cds_start": 3265,
"cds_end": null,
"cds_length": 3693,
"cdna_start": 3491,
"cdna_end": null,
"cdna_length": 4954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOF",
"gene_hgnc_id": 8515,
"hgvs_c": "c.5566C>T",
"hgvs_p": "p.Arg1856Trp",
"transcript": "NM_001287489.2",
"protein_id": "NP_001274418.1",
"transcript_support_level": null,
"aa_start": 1856,
"aa_end": null,
"aa_length": 1997,
"cds_start": 5566,
"cds_end": null,
"cds_length": 5994,
"cdna_start": 5751,
"cdna_end": null,
"cdna_length": 7016,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOF",
"gene_hgnc_id": 8515,
"hgvs_c": "c.5566C>T",
"hgvs_p": "p.Arg1856Trp",
"transcript": "ENST00000403946.7",
"protein_id": "ENSP00000385255.3",
"transcript_support_level": 5,
"aa_start": 1856,
"aa_end": null,
"aa_length": 1997,
"cds_start": 5566,
"cds_end": null,
"cds_length": 5994,
"cdna_start": 5673,
"cdna_end": null,
"cdna_length": 6937,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOF",
"gene_hgnc_id": 8515,
"hgvs_c": "c.3496C>T",
"hgvs_p": "p.Arg1166Trp",
"transcript": "NM_194322.3",
"protein_id": "NP_919303.1",
"transcript_support_level": null,
"aa_start": 1166,
"aa_end": null,
"aa_length": 1307,
"cds_start": 3496,
"cds_end": null,
"cds_length": 3924,
"cdna_start": 3727,
"cdna_end": null,
"cdna_length": 5190,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOF",
"gene_hgnc_id": 8515,
"hgvs_c": "c.3265C>T",
"hgvs_p": "p.Arg1089Trp",
"transcript": "NM_004802.4",
"protein_id": "NP_004793.2",
"transcript_support_level": null,
"aa_start": 1089,
"aa_end": null,
"aa_length": 1230,
"cds_start": 3265,
"cds_end": null,
"cds_length": 3693,
"cdna_start": 3573,
"cdna_end": null,
"cdna_length": 5036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OTOF",
"gene_hgnc_id": 8515,
"dbsnp": "rs368155547",
"frequency_reference_population": 0.000022313543,
"hom_count_reference_population": 0,
"allele_count_reference_population": 36,
"gnomad_exomes_af": 0.0000205279,
"gnomad_genomes_af": 0.0000394882,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9100342392921448,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.723,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9104,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.34,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.053,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PM5",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000272371.7",
"gene_symbol": "OTOF",
"hgnc_id": 8515,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.5566C>T",
"hgvs_p": "p.Arg1856Trp"
}
],
"clinvar_disease": "Autosomal recessive nonsyndromic hearing loss 9,OTOF-related disorder,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 US:2",
"phenotype_combined": "not specified|not provided|OTOF-related disorder|Autosomal recessive nonsyndromic hearing loss 9",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}