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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: 13-20189605-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=20189605&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 20189605,
"ref": "T",
"alt": "G",
"effect": "splice_acceptor_variant,intron_variant",
"transcript": "ENST00000382848.5",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.-22-2A>C",
"hgvs_p": null,
"transcript": "NM_004004.6",
"protein_id": "NP_003995.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 226,
"cds_start": -4,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2290,
"mane_select": "ENST00000382848.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.-22-2A>C",
"hgvs_p": null,
"transcript": "ENST00000382848.5",
"protein_id": "ENSP00000372299.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 226,
"cds_start": -4,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2290,
"mane_select": "NM_004004.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_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.-24A>C",
"hgvs_p": null,
"transcript": "ENST00000382844.2",
"protein_id": "ENSP00000372295.1",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 226,
"cds_start": -4,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2318,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000296095",
"gene_hgnc_id": null,
"hgvs_c": "n.232-4025A>C",
"hgvs_p": null,
"transcript": "ENST00000736390.1",
"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": 732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"hgvs_c": "c.-22-2A>C",
"hgvs_p": null,
"transcript": "XM_011535049.3",
"protein_id": "XP_011533351.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 226,
"cds_start": -4,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GJB2",
"gene_hgnc_id": 4284,
"dbsnp": "rs201895089",
"frequency_reference_population": 0.00069773773,
"hom_count_reference_population": 2,
"allele_count_reference_population": 1122,
"gnomad_exomes_af": 0.000710285,
"gnomad_genomes_af": 0.000577807,
"gnomad_exomes_ac": 1034,
"gnomad_genomes_ac": 88,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.44999998807907104,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9240000247955322,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.715,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.91,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999978952611685,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "BS1,PS3_Supporting,PP1,PM3",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 4,
"pathogenic_score": 4,
"criteria": [
"BS1",
"PS3_Supporting",
"PP1",
"PM3"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000382848.5",
"gene_symbol": "GJB2",
"hgnc_id": 4284,
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.-22-2A>C",
"hgvs_p": null
},
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000736390.1",
"gene_symbol": "ENSG00000296095",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.232-4025A>C",
"hgvs_p": null
}
],
"clinvar_disease": " deafness AND leukonychia syndrome, hystrix-like, with hearing loss,7 conditions,Autosomal dominant nonsyndromic hearing loss 3A,Autosomal recessive nonsyndromic hearing loss 1A,GJB2-related disorder,Ichthyosis,Knuckle pads,Mutilating keratoderma,Nonsyndromic genetic hearing loss,Palmoplantar keratoderma-deafness syndrome,not provided,not specified",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:6 LP:12 US:1 B:2",
"phenotype_combined": "Autosomal recessive nonsyndromic hearing loss 1A|Nonsyndromic genetic hearing loss|Autosomal dominant nonsyndromic hearing loss 3A|not provided|not specified|Ichthyosis, hystrix-like, with hearing loss|7 conditions|GJB2-related disorder|Mutilating keratoderma;Palmoplantar keratoderma-deafness syndrome;Knuckle pads, deafness AND leukonychia syndrome",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}