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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: 3-8745688-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=8745688&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 8745688,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000343849.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"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.277G>A",
"hgvs_p": "p.Ala93Thr",
"transcript": "NM_033337.3",
"protein_id": "NP_203123.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 151,
"cds_start": 277,
"cds_end": null,
"cds_length": 456,
"cdna_start": 352,
"cdna_end": null,
"cdna_length": 1422,
"mane_select": "ENST00000343849.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"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.277G>A",
"hgvs_p": "p.Ala93Thr",
"transcript": "ENST00000343849.3",
"protein_id": "ENSP00000341940.2",
"transcript_support_level": 1,
"aa_start": 93,
"aa_end": null,
"aa_length": 151,
"cds_start": 277,
"cds_end": null,
"cds_length": 456,
"cdna_start": 352,
"cdna_end": null,
"cdna_length": 1422,
"mane_select": "NM_033337.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"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.277G>A",
"hgvs_p": "p.Ala93Thr",
"transcript": "ENST00000397368.2",
"protein_id": "ENSP00000380525.2",
"transcript_support_level": 1,
"aa_start": 93,
"aa_end": null,
"aa_length": 151,
"cds_start": 277,
"cds_end": null,
"cds_length": 456,
"cdna_start": 288,
"cdna_end": null,
"cdna_length": 1260,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"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.277G>A",
"hgvs_p": "p.Ala93Thr",
"transcript": "NM_001234.5",
"protein_id": "NP_001225.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 151,
"cds_start": 277,
"cds_end": null,
"cds_length": 456,
"cdna_start": 352,
"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+11698G>A",
"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.1885-3086C>T",
"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": "rs28936686",
"frequency_reference_population": 0.00010285147,
"hom_count_reference_population": 0,
"allele_count_reference_population": 166,
"gnomad_exomes_af": 0.000109453,
"gnomad_genomes_af": 0.0000394306,
"gnomad_exomes_ac": 160,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9817986488342285,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.982,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9469,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.59,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.519,
"phylop100way_prediction": "Pathogenic",
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PP2,PP3_Strong,PP5,BS1_Supporting",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 1,
"pathogenic_score": 8,
"criteria": [
"PM1",
"PP2",
"PP3_Strong",
"PP5",
"BS1_Supporting"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000343849.3",
"gene_symbol": "CAV3",
"hgnc_id": 1529,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.277G>A",
"hgvs_p": "p.Ala93Thr"
},
{
"score": 1,
"benign_score": 4,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007095681.1",
"gene_symbol": "OXTR",
"hgnc_id": 8529,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "n.1885-3086C>T",
"hgvs_p": null
}
],
"clinvar_disease": " Tateyama type, autosomal recessive,Cardiovascular phenotype,Caveolinopathy,Distal myopathy,Elevated circulating creatine kinase concentration,Hypertrophic cardiomyopathy 1,Long QT syndrome,Long QT syndrome 9,Rippling muscle disease 2,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:5 LP:6 US:1 O:1",
"phenotype_combined": "Rippling muscle disease 2, autosomal recessive|not provided|Long QT syndrome|Cardiovascular phenotype|Rippling muscle disease 2|Hypertrophic cardiomyopathy 1|Elevated circulating creatine kinase concentration;Hypertrophic cardiomyopathy 1;Distal myopathy, Tateyama type;Rippling muscle disease 2;Long QT syndrome 9|Caveolinopathy",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}