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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: 10-71732196-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=71732196&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 71732196,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000224721.12",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.3925G>A",
"hgvs_p": "p.Glu1309Lys",
"transcript": "NM_022124.6",
"protein_id": "NP_071407.4",
"transcript_support_level": null,
"aa_start": 1309,
"aa_end": null,
"aa_length": 3354,
"cds_start": 3925,
"cds_end": null,
"cds_length": 10065,
"cdna_start": 4329,
"cdna_end": null,
"cdna_length": 11138,
"mane_select": "ENST00000224721.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.3925G>A",
"hgvs_p": "p.Glu1309Lys",
"transcript": "ENST00000224721.12",
"protein_id": "ENSP00000224721.9",
"transcript_support_level": 5,
"aa_start": 1309,
"aa_end": null,
"aa_length": 3354,
"cds_start": 3925,
"cds_end": null,
"cds_length": 10065,
"cdna_start": 4329,
"cdna_end": null,
"cdna_length": 11138,
"mane_select": "NM_022124.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.3925G>A",
"hgvs_p": "p.Glu1309Lys",
"transcript": "NM_001171930.2",
"protein_id": "NP_001165401.1",
"transcript_support_level": null,
"aa_start": 1309,
"aa_end": null,
"aa_length": 1381,
"cds_start": 3925,
"cds_end": null,
"cds_length": 4146,
"cdna_start": 4329,
"cdna_end": null,
"cdna_length": 4858,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.3925G>A",
"hgvs_p": "p.Glu1309Lys",
"transcript": "ENST00000616684.4",
"protein_id": "ENSP00000482036.2",
"transcript_support_level": 5,
"aa_start": 1309,
"aa_end": null,
"aa_length": 1381,
"cds_start": 3925,
"cds_end": null,
"cds_length": 4146,
"cdna_start": 4287,
"cdna_end": null,
"cdna_length": 4814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "c.3922G>A",
"hgvs_p": "p.Glu1308Lys",
"transcript": "ENST00000398809.9",
"protein_id": "ENSP00000381789.5",
"transcript_support_level": 5,
"aa_start": 1308,
"aa_end": null,
"aa_length": 1380,
"cds_start": 3922,
"cds_end": null,
"cds_length": 4143,
"cdna_start": 4312,
"cdna_end": null,
"cdna_length": 4839,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"hgvs_c": "n.617G>A",
"hgvs_p": null,
"transcript": "ENST00000398792.3",
"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": 1649,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "C10orf105",
"gene_hgnc_id": 20304,
"hgvs_c": "c.-6+5532C>T",
"hgvs_p": null,
"transcript": "NM_001168390.2",
"protein_id": "NP_001161862.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 133,
"cds_start": -4,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4765,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "C10orf105",
"gene_hgnc_id": 20304,
"hgvs_c": "c.-6+5532C>T",
"hgvs_p": null,
"transcript": "ENST00000398786.2",
"protein_id": "ENSP00000381766.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 133,
"cds_start": -4,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CDH23",
"gene_hgnc_id": 13733,
"dbsnp": "rs111033468",
"frequency_reference_population": 0.000002736813,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273681,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7572649717330933,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.32,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4764,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.36,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.623,
"phylop100way_prediction": "Pathogenic",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000224721.12",
"gene_symbol": "CDH23",
"hgnc_id": 13733,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3925G>A",
"hgvs_p": "p.Glu1309Lys"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001168390.2",
"gene_symbol": "C10orf105",
"hgnc_id": 20304,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-6+5532C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Usher syndrome type 1,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not specified|Usher syndrome type 1|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}