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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: 13-20189473-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=20189473&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 20189473,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004004.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Val37Ile",
"transcript": "NM_004004.6",
"protein_id": "NP_003995.2",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 226,
"cds_start": 109,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000382848.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004004.6"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Val37Ile",
"transcript": "ENST00000382848.5",
"protein_id": "ENSP00000372299.4",
"transcript_support_level": 1,
"aa_start": 37,
"aa_end": null,
"aa_length": 226,
"cds_start": 109,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004004.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000382848.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Val37Ile",
"transcript": "ENST00000382844.2",
"protein_id": "ENSP00000372295.1",
"transcript_support_level": 6,
"aa_start": 37,
"aa_end": null,
"aa_length": 226,
"cds_start": 109,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000382844.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Val37Ile",
"transcript": "ENST00000906230.1",
"protein_id": "ENSP00000576289.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 226,
"cds_start": 109,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906230.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Val37Ile",
"transcript": "ENST00000906231.1",
"protein_id": "ENSP00000576290.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 226,
"cds_start": 109,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906231.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Val37Ile",
"transcript": "ENST00000906232.1",
"protein_id": "ENSP00000576291.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 226,
"cds_start": 109,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906232.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Val37Ile",
"transcript": "ENST00000906233.1",
"protein_id": "ENSP00000576292.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 226,
"cds_start": 109,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906233.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Val37Ile",
"transcript": "ENST00000906234.1",
"protein_id": "ENSP00000576293.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 226,
"cds_start": 109,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906234.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Val37Ile",
"transcript": "ENST00000906235.1",
"protein_id": "ENSP00000576294.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 226,
"cds_start": 109,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906235.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Val37Ile",
"transcript": "ENST00000906236.1",
"protein_id": "ENSP00000576295.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 226,
"cds_start": 109,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906236.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Val37Ile",
"transcript": "ENST00000957350.1",
"protein_id": "ENSP00000627409.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 226,
"cds_start": 109,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957350.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Val37Ile",
"transcript": "XM_011535049.3",
"protein_id": "XP_011533351.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 226,
"cds_start": 109,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011535049.3"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000296095",
"gene_hgnc_id": null,
"hgvs_c": "n.232-3893G>A",
"hgvs_p": null,
"transcript": "ENST00000736390.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000736390.1"
}
],
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"dbsnp": "rs72474224",
"frequency_reference_population": 0.0025227957,
"hom_count_reference_population": 101,
"allele_count_reference_population": 4071,
"gnomad_exomes_af": 0.00236898,
"gnomad_genomes_af": 0.00399879,
"gnomad_exomes_ac": 3462,
"gnomad_genomes_ac": 609,
"gnomad_exomes_homalt": 83,
"gnomad_genomes_homalt": 18,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009643405675888062,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.656,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1558,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.102,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS4,PP1_Strong,PM3",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PS4",
"PP1_Strong",
"PM3"
],
"verdict": "Pathogenic",
"transcript": "NM_004004.6",
"gene_symbol": "GJB2",
"hgnc_id": 4284,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Val37Ile"
},
{
"score": 6,
"benign_score": 2,
"pathogenic_score": 8,
"criteria": [
"PP5_Very_Strong",
"BP4",
"BS1_Supporting"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000736390.1",
"gene_symbol": "ENSG00000296095",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.232-3893G>A",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive, deafness AND leukonychia syndrome,7 conditions,Autosomal dominant nonsyndromic hearing loss 3A,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal recessive nonsyndromic hearing loss 1B,GJB2-related disorder,Hearing impairment,Hearing loss,Inborn genetic diseases,Knuckle pads,Mutilating keratoderma,Nonsyndromic Deafness,Nonsyndromic genetic hearing loss,Palmoplantar keratoderma-deafness syndrome,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:39 LP:4 US:1 LB:1 O:1",
"phenotype_combined": "Autosomal recessive nonsyndromic hearing loss 1A|not provided|Hearing impairment|Autosomal dominant nonsyndromic hearing loss 3A|Autosomal recessive nonsyndromic hearing loss 1B;Autosomal recessive nonsyndromic hearing loss 1A|Nonsyndromic genetic hearing loss|Nonsyndromic Deafness|7 conditions|Inborn genetic diseases|GJB2-related disorder|Hearing loss, autosomal recessive|Mutilating keratoderma;Palmoplantar keratoderma-deafness syndrome;Knuckle pads, deafness AND leukonychia syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}