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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: 13-20189511-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=20189511&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PS3",
"BS1",
"PVS1",
"PM3"
],
"effects": [
"stop_gained"
],
"gene_symbol": "GJB2",
"hgnc_id": 4284,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Trp24*",
"inheritance_mode": "AD,AR",
"pathogenic_score": 14,
"score": 10,
"transcript": "NM_004004.6",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000296095",
"hgnc_id": null,
"hgvs_c": "n.232-3931G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 14,
"score": 14,
"transcript": "ENST00000736390.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,BS1,PVS1,PM3",
"acmg_score": 10,
"allele_count_reference_population": 451,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.57,
"chr": "13",
"clinvar_classification": "Pathogenic",
"clinvar_disease": " autosomal recessive, deafness AND leukonychia syndrome, hystrix-like, with hearing loss,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,Hereditary palmoplantar keratoderma,Ichthyosis,Knuckle pads,Mutilating keratoderma,Nonsyndromic genetic hearing loss,Palmoplantar keratoderma-deafness syndrome,Rare genetic deafness,Sensorineural hearing loss disorder,not provided",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:37 LB:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.5699999928474426,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 226,
"aa_ref": "W",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2290,
"cdna_start": 249,
"cds_end": null,
"cds_length": 681,
"cds_start": 71,
"consequences": [
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_004004.6",
"gene_hgnc_id": 4284,
"gene_symbol": "GJB2",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Trp24*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000382848.5",
"protein_coding": true,
"protein_id": "NP_003995.2",
"strand": false,
"transcript": "NM_004004.6",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 226,
"aa_ref": "W",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2290,
"cdna_start": 249,
"cds_end": null,
"cds_length": 681,
"cds_start": 71,
"consequences": [
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000382848.5",
"gene_hgnc_id": 4284,
"gene_symbol": "GJB2",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Trp24*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004004.6",
"protein_coding": true,
"protein_id": "ENSP00000372299.4",
"strand": false,
"transcript": "ENST00000382848.5",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 226,
"aa_ref": "W",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2318,
"cdna_start": 270,
"cds_end": null,
"cds_length": 681,
"cds_start": 71,
"consequences": [
"stop_gained"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000382844.2",
"gene_hgnc_id": 4284,
"gene_symbol": "GJB2",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Trp24*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000372295.1",
"strand": false,
"transcript": "ENST00000382844.2",
"transcript_support_level": 6
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 226,
"aa_ref": "W",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2311,
"cdna_start": 326,
"cds_end": null,
"cds_length": 681,
"cds_start": 71,
"consequences": [
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000906230.1",
"gene_hgnc_id": 4284,
"gene_symbol": "GJB2",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Trp24*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576289.1",
"strand": false,
"transcript": "ENST00000906230.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 226,
"aa_ref": "W",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2913,
"cdna_start": 877,
"cds_end": null,
"cds_length": 681,
"cds_start": 71,
"consequences": [
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000906231.1",
"gene_hgnc_id": 4284,
"gene_symbol": "GJB2",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Trp24*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576290.1",
"strand": false,
"transcript": "ENST00000906231.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 226,
"aa_ref": "W",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1991,
"cdna_start": 283,
"cds_end": null,
"cds_length": 681,
"cds_start": 71,
"consequences": [
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000906232.1",
"gene_hgnc_id": 4284,
"gene_symbol": "GJB2",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Trp24*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576291.1",
"strand": false,
"transcript": "ENST00000906232.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 226,
"aa_ref": "W",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2849,
"cdna_start": 813,
"cds_end": null,
"cds_length": 681,
"cds_start": 71,
"consequences": [
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000906233.1",
"gene_hgnc_id": 4284,
"gene_symbol": "GJB2",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Trp24*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576292.1",
"strand": false,
"transcript": "ENST00000906233.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 226,
"aa_ref": "W",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1874,
"cdna_start": 165,
"cds_end": null,
"cds_length": 681,
"cds_start": 71,
"consequences": [
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000906234.1",
"gene_hgnc_id": 4284,
"gene_symbol": "GJB2",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Trp24*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576293.1",
"strand": false,
"transcript": "ENST00000906234.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 226,
"aa_ref": "W",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2869,
"cdna_start": 833,
"cds_end": null,
"cds_length": 681,
"cds_start": 71,
"consequences": [
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000906235.1",
"gene_hgnc_id": 4284,
"gene_symbol": "GJB2",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Trp24*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576294.1",
"strand": false,
"transcript": "ENST00000906235.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 226,
"aa_ref": "W",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2040,
"cdna_start": 331,
"cds_end": null,
"cds_length": 681,
"cds_start": 71,
"consequences": [
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000906236.1",
"gene_hgnc_id": 4284,
"gene_symbol": "GJB2",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Trp24*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576295.1",
"strand": false,
"transcript": "ENST00000906236.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 226,
"aa_ref": "W",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2330,
"cdna_start": 289,
"cds_end": null,
"cds_length": 681,
"cds_start": 71,
"consequences": [
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000957350.1",
"gene_hgnc_id": 4284,
"gene_symbol": "GJB2",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Trp24*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627409.1",
"strand": false,
"transcript": "ENST00000957350.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 226,
"aa_ref": "W",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3112,
"cdna_start": 1071,
"cds_end": null,
"cds_length": 681,
"cds_start": 71,
"consequences": [
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_011535049.3",
"gene_hgnc_id": 4284,
"gene_symbol": "GJB2",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Trp24*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011533351.1",
"strand": false,
"transcript": "XM_011535049.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 732,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000736390.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000296095",
"hgvs_c": "n.232-3931G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000736390.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs104894396",
"effect": "stop_gained",
"frequency_reference_population": 0.00027939884,
"gene_hgnc_id": 4284,
"gene_symbol": "GJB2",
"gnomad_exomes_ac": 430,
"gnomad_exomes_af": 0.000294141,
"gnomad_exomes_homalt": 4,
"gnomad_genomes_ac": 21,
"gnomad_genomes_af": 0.000137889,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 4,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Autosomal recessive nonsyndromic hearing loss 1A|Hearing impairment|Nonsyndromic genetic hearing loss|Rare genetic deafness|Ichthyosis, hystrix-like, with hearing loss|Autosomal dominant nonsyndromic hearing loss 3A|not provided|Hearing loss|Autosomal recessive nonsyndromic hearing loss 1B;Autosomal recessive nonsyndromic hearing loss 1A|Palmoplantar keratoderma-deafness syndrome|Hearing loss, autosomal recessive|Knuckle pads, deafness AND leukonychia syndrome|Mutilating keratoderma|Hereditary palmoplantar keratoderma|7 conditions|GJB2-related disorder|Sensorineural hearing loss disorder",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.854,
"pos": 20189511,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004004.6"
}
]
}