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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: 10-71705007-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=71705007&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 71705007,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000224721.12",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.2830A>G",
"hgvs_p": "p.Ser944Gly",
"transcript": "NM_022124.6",
"protein_id": "NP_071407.4",
"transcript_support_level": null,
"aa_start": 944,
"aa_end": null,
"aa_length": 3354,
"cds_start": 2830,
"cds_end": null,
"cds_length": 10065,
"cdna_start": 3234,
"cdna_end": null,
"cdna_length": 11138,
"mane_select": "ENST00000224721.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.2830A>G",
"hgvs_p": "p.Ser944Gly",
"transcript": "ENST00000224721.12",
"protein_id": "ENSP00000224721.9",
"transcript_support_level": 5,
"aa_start": 944,
"aa_end": null,
"aa_length": 3354,
"cds_start": 2830,
"cds_end": null,
"cds_length": 10065,
"cdna_start": 3234,
"cdna_end": null,
"cdna_length": 11138,
"mane_select": "NM_022124.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.2830A>G",
"hgvs_p": "p.Ser944Gly",
"transcript": "NM_001171930.2",
"protein_id": "NP_001165401.1",
"transcript_support_level": null,
"aa_start": 944,
"aa_end": null,
"aa_length": 1381,
"cds_start": 2830,
"cds_end": null,
"cds_length": 4146,
"cdna_start": 3234,
"cdna_end": null,
"cdna_length": 4858,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.2830A>G",
"hgvs_p": "p.Ser944Gly",
"transcript": "ENST00000616684.4",
"protein_id": "ENSP00000482036.2",
"transcript_support_level": 5,
"aa_start": 944,
"aa_end": null,
"aa_length": 1381,
"cds_start": 2830,
"cds_end": null,
"cds_length": 4146,
"cdna_start": 3192,
"cdna_end": null,
"cdna_length": 4814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.2830A>G",
"hgvs_p": "p.Ser944Gly",
"transcript": "ENST00000398809.9",
"protein_id": "ENSP00000381789.5",
"transcript_support_level": 5,
"aa_start": 944,
"aa_end": null,
"aa_length": 1380,
"cds_start": 2830,
"cds_end": null,
"cds_length": 4143,
"cdna_start": 3220,
"cdna_end": null,
"cdna_length": 4839,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.2830A>G",
"hgvs_p": "p.Ser944Gly",
"transcript": "ENST00000442677.4",
"protein_id": "ENSP00000388894.3",
"transcript_support_level": 5,
"aa_start": 944,
"aa_end": null,
"aa_length": 1211,
"cds_start": 2830,
"cds_end": null,
"cds_length": 3636,
"cdna_start": 2830,
"cdna_end": null,
"cdna_length": 8225,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.2830A>G",
"hgvs_p": "p.Ser944Gly",
"transcript": "NM_001171931.2",
"protein_id": "NP_001165402.1",
"transcript_support_level": null,
"aa_start": 944,
"aa_end": null,
"aa_length": 1061,
"cds_start": 2830,
"cds_end": null,
"cds_length": 3186,
"cdna_start": 3234,
"cdna_end": null,
"cdna_length": 3971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.2830A>G",
"hgvs_p": "p.Ser944Gly",
"transcript": "ENST00000299366.11",
"protein_id": "ENSP00000299366.8",
"transcript_support_level": 5,
"aa_start": 944,
"aa_end": null,
"aa_length": 1061,
"cds_start": 2830,
"cds_end": null,
"cds_length": 3186,
"cdna_start": 3217,
"cdna_end": null,
"cdna_length": 3954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.2260A>G",
"hgvs_p": "p.Ser754Gly",
"transcript": "ENST00000466757.8",
"protein_id": "ENSP00000473539.2",
"transcript_support_level": 5,
"aa_start": 754,
"aa_end": null,
"aa_length": 1034,
"cds_start": 2260,
"cds_end": null,
"cds_length": 3105,
"cdna_start": 2261,
"cdna_end": null,
"cdna_length": 4471,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000300551",
"gene_hgnc_id": null,
"hgvs_c": "n.244-412T>C",
"hgvs_p": null,
"transcript": "ENST00000772671.1",
"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": 415,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"dbsnp": "rs188098974",
"frequency_reference_population": 0.0010175457,
"hom_count_reference_population": 9,
"allele_count_reference_population": 1641,
"gnomad_exomes_af": 0.00102496,
"gnomad_genomes_af": 0.00094641,
"gnomad_exomes_ac": 1497,
"gnomad_genomes_ac": 144,
"gnomad_exomes_homalt": 7,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01838386058807373,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.183,
"revel_prediction": "Benign",
"alphamissense_score": 0.1143,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.157,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000224721.12",
"gene_symbol": "CDH23",
"hgnc_id": 13733,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2830A>G",
"hgvs_p": "p.Ser944Gly"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000772671.1",
"gene_symbol": "ENSG00000300551",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.244-412T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal recessive nonsyndromic hearing loss 12,Usher syndrome type 1,Usher syndrome type 1D,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:2 B:2",
"phenotype_combined": "not specified|not provided|Usher syndrome type 1D|Autosomal recessive nonsyndromic hearing loss 12|Usher syndrome type 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}