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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: 16-21722978-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=21722978&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 21722978,
"ref": "C",
"alt": "G",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000646100.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"hgvs_c": "c.1880C>G",
"hgvs_p": "p.Pro627Arg",
"transcript": "NM_144672.4",
"protein_id": "NP_653273.3",
"transcript_support_level": null,
"aa_start": 627,
"aa_end": null,
"aa_length": 1139,
"cds_start": 1880,
"cds_end": null,
"cds_length": 3420,
"cdna_start": 2149,
"cdna_end": null,
"cdna_length": 3878,
"mane_select": "ENST00000646100.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"hgvs_c": "c.1880C>G",
"hgvs_p": "p.Pro627Arg",
"transcript": "ENST00000646100.2",
"protein_id": "ENSP00000496564.2",
"transcript_support_level": null,
"aa_start": 627,
"aa_end": null,
"aa_length": 1139,
"cds_start": 1880,
"cds_end": null,
"cds_length": 3420,
"cdna_start": 2149,
"cdna_end": null,
"cdna_length": 3878,
"mane_select": "NM_144672.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"hgvs_c": "c.1880C>G",
"hgvs_p": "p.Pro627Arg",
"transcript": "ENST00000388958.8",
"protein_id": "ENSP00000373610.3",
"transcript_support_level": 1,
"aa_start": 627,
"aa_end": null,
"aa_length": 1139,
"cds_start": 1880,
"cds_end": null,
"cds_length": 3420,
"cdna_start": 1881,
"cdna_end": null,
"cdna_length": 3609,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"hgvs_c": "c.1922C>G",
"hgvs_p": "p.Pro641Arg",
"transcript": "ENST00000286149.8",
"protein_id": "ENSP00000286149.4",
"transcript_support_level": 5,
"aa_start": 641,
"aa_end": null,
"aa_length": 1153,
"cds_start": 1922,
"cds_end": null,
"cds_length": 3462,
"cdna_start": 1923,
"cdna_end": null,
"cdna_length": 3471,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"hgvs_c": "c.1643C>G",
"hgvs_p": "p.Pro548Arg",
"transcript": "NM_001161683.2",
"protein_id": "NP_001155155.1",
"transcript_support_level": null,
"aa_start": 548,
"aa_end": null,
"aa_length": 1060,
"cds_start": 1643,
"cds_end": null,
"cds_length": 3183,
"cdna_start": 1737,
"cdna_end": null,
"cdna_length": 3466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"hgvs_c": "c.1643C>G",
"hgvs_p": "p.Pro548Arg",
"transcript": "ENST00000388956.8",
"protein_id": "ENSP00000373608.4",
"transcript_support_level": 2,
"aa_start": 548,
"aa_end": null,
"aa_length": 1060,
"cds_start": 1643,
"cds_end": null,
"cds_length": 3183,
"cdna_start": 1737,
"cdna_end": null,
"cdna_length": 3466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"hgvs_c": "c.908C>G",
"hgvs_p": "p.Pro303Arg",
"transcript": "NM_170664.3",
"protein_id": "NP_733764.1",
"transcript_support_level": null,
"aa_start": 303,
"aa_end": null,
"aa_length": 815,
"cds_start": 908,
"cds_end": null,
"cds_length": 2448,
"cdna_start": 975,
"cdna_end": null,
"cdna_length": 2704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"hgvs_c": "c.908C>G",
"hgvs_p": "p.Pro303Arg",
"transcript": "ENST00000388957.3",
"protein_id": "ENSP00000373609.3",
"transcript_support_level": 2,
"aa_start": 303,
"aa_end": null,
"aa_length": 815,
"cds_start": 908,
"cds_end": null,
"cds_length": 2448,
"cdna_start": 975,
"cdna_end": null,
"cdna_length": 2703,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"hgvs_c": "c.749C>G",
"hgvs_p": "p.Pro250Arg",
"transcript": "XM_011545748.3",
"protein_id": "XP_011544050.3",
"transcript_support_level": null,
"aa_start": 250,
"aa_end": null,
"aa_length": 762,
"cds_start": 749,
"cds_end": null,
"cds_length": 2289,
"cdna_start": 919,
"cdna_end": null,
"cdna_length": 2648,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"hgvs_c": "n.1295C>G",
"hgvs_p": null,
"transcript": "ENST00000563871.5",
"protein_id": null,
"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": 4635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"hgvs_c": "n.*694C>G",
"hgvs_p": null,
"transcript": "ENST00000647277.1",
"protein_id": "ENSP00000495594.1",
"transcript_support_level": null,
"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": 3385,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"hgvs_c": "n.975C>G",
"hgvs_p": null,
"transcript": "XR_002957775.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2043,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"hgvs_c": "n.*694C>G",
"hgvs_p": null,
"transcript": "ENST00000647277.1",
"protein_id": "ENSP00000495594.1",
"transcript_support_level": null,
"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": 3385,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OTOA",
"gene_hgnc_id": 16378,
"dbsnp": "rs727503351",
"frequency_reference_population": 0.0000034207214,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000342072,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8179301619529724,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.4339999854564667,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.64,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7607,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.24,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.258,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.569740964921985,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3,PP5",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PM5",
"PP3",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000646100.2",
"gene_symbol": "OTOA",
"hgnc_id": 16378,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1880C>G",
"hgvs_p": "p.Pro627Arg"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}