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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: 3-8745627-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=8745627&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 8745627,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000343849.3",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAV3",
"gene_hgnc_id": 1529,
"hgvs_c": "c.216C>G",
"hgvs_p": "p.Cys72Trp",
"transcript": "NM_033337.3",
"protein_id": "NP_203123.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 151,
"cds_start": 216,
"cds_end": null,
"cds_length": 456,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 1422,
"mane_select": "ENST00000343849.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAV3",
"gene_hgnc_id": 1529,
"hgvs_c": "c.216C>G",
"hgvs_p": "p.Cys72Trp",
"transcript": "ENST00000343849.3",
"protein_id": "ENSP00000341940.2",
"transcript_support_level": 1,
"aa_start": 72,
"aa_end": null,
"aa_length": 151,
"cds_start": 216,
"cds_end": null,
"cds_length": 456,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 1422,
"mane_select": "NM_033337.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAV3",
"gene_hgnc_id": 1529,
"hgvs_c": "c.216C>G",
"hgvs_p": "p.Cys72Trp",
"transcript": "ENST00000397368.2",
"protein_id": "ENSP00000380525.2",
"transcript_support_level": 1,
"aa_start": 72,
"aa_end": null,
"aa_length": 151,
"cds_start": 216,
"cds_end": null,
"cds_length": 456,
"cdna_start": 227,
"cdna_end": null,
"cdna_length": 1260,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAV3",
"gene_hgnc_id": 1529,
"hgvs_c": "c.216C>G",
"hgvs_p": "p.Cys72Trp",
"transcript": "NM_001234.5",
"protein_id": "NP_001225.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 151,
"cds_start": 216,
"cds_end": null,
"cds_length": 456,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 1326,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CAV3",
"gene_hgnc_id": 1529,
"hgvs_c": "n.155+11637C>G",
"hgvs_p": null,
"transcript": "ENST00000472766.1",
"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": 680,
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "OXTR",
"gene_hgnc_id": 8529,
"hgvs_c": "n.1885-3025G>C",
"hgvs_p": null,
"transcript": "XR_007095681.1",
"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": 3218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CAV3",
"gene_hgnc_id": 1529,
"dbsnp": "rs116840776",
"frequency_reference_population": 0.0021733043,
"hom_count_reference_population": 10,
"allele_count_reference_population": 3508,
"gnomad_exomes_af": 0.00222463,
"gnomad_genomes_af": 0.00168072,
"gnomad_exomes_ac": 3252,
"gnomad_genomes_ac": 256,
"gnomad_exomes_homalt": 8,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.26156944036483765,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.773,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9037,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.38,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.131,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": "Benign",
"acmg_criteria": "PP2,BP4_Moderate,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 11,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Moderate",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000343849.3",
"gene_symbol": "CAV3",
"hgnc_id": 1529,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.216C>G",
"hgvs_p": "p.Cys72Trp"
},
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "XR_007095681.1",
"gene_symbol": "OXTR",
"hgnc_id": 8529,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "n.1885-3025G>C",
"hgvs_p": null
}
],
"clinvar_disease": " Tateyama type,CAV3-related disorder,Cardiomyopathy,Cardiovascular phenotype,Caveolinopathy,Distal myopathy,Elevated circulating creatine kinase concentration,Hypertrophic cardiomyopathy 1,Limb-girdle muscular dystrophy,Long QT syndrome,Long QT syndrome 1,Long QT syndrome 9,Rippling muscle disease 2,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:9 B:6 O:1",
"phenotype_combined": "Rippling muscle disease 2|not provided|not specified|Limb-girdle muscular dystrophy|Cardiovascular phenotype|Elevated circulating creatine kinase concentration;Hypertrophic cardiomyopathy 1;Distal myopathy, Tateyama type;Rippling muscle disease 2;Long QT syndrome 9|Cardiomyopathy|Long QT syndrome|Caveolinopathy|Long QT syndrome 1|CAV3-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}