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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: 3-58534958-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=58534958&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 58534958,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000302819.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACOX2",
"gene_hgnc_id": 120,
"hgvs_c": "c.149G>T",
"hgvs_p": "p.Arg50Leu",
"transcript": "NM_003500.4",
"protein_id": "NP_003491.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 681,
"cds_start": 149,
"cds_end": null,
"cds_length": 2046,
"cdna_start": 312,
"cdna_end": null,
"cdna_length": 2297,
"mane_select": "ENST00000302819.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACOX2",
"gene_hgnc_id": 120,
"hgvs_c": "c.149G>T",
"hgvs_p": "p.Arg50Leu",
"transcript": "ENST00000302819.10",
"protein_id": "ENSP00000307697.5",
"transcript_support_level": 1,
"aa_start": 50,
"aa_end": null,
"aa_length": 681,
"cds_start": 149,
"cds_end": null,
"cds_length": 2046,
"cdna_start": 312,
"cdna_end": null,
"cdna_length": 2297,
"mane_select": "NM_003500.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACOX2",
"gene_hgnc_id": 120,
"hgvs_c": "c.149G>T",
"hgvs_p": "p.Arg50Leu",
"transcript": "ENST00000459701.6",
"protein_id": "ENSP00000418562.2",
"transcript_support_level": 5,
"aa_start": 50,
"aa_end": null,
"aa_length": 667,
"cds_start": 149,
"cds_end": null,
"cds_length": 2004,
"cdna_start": 405,
"cdna_end": null,
"cdna_length": 2348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACOX2",
"gene_hgnc_id": 120,
"hgvs_c": "c.149G>T",
"hgvs_p": "p.Arg50Leu",
"transcript": "ENST00000474098.1",
"protein_id": "ENSP00000419927.1",
"transcript_support_level": 3,
"aa_start": 50,
"aa_end": null,
"aa_length": 170,
"cds_start": 149,
"cds_end": null,
"cds_length": 514,
"cdna_start": 343,
"cdna_end": null,
"cdna_length": 708,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACOX2",
"gene_hgnc_id": 120,
"hgvs_c": "c.347G>T",
"hgvs_p": "p.Arg116Leu",
"transcript": "XM_047449042.1",
"protein_id": "XP_047304998.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 747,
"cds_start": 347,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 1191,
"cdna_end": null,
"cdna_length": 3176,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACOX2",
"gene_hgnc_id": 120,
"hgvs_c": "c.149G>T",
"hgvs_p": "p.Arg50Leu",
"transcript": "XM_005265505.2",
"protein_id": "XP_005265562.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 681,
"cds_start": 149,
"cds_end": null,
"cds_length": 2046,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 2340,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACOX2",
"gene_hgnc_id": 120,
"hgvs_c": "n.297G>T",
"hgvs_p": null,
"transcript": "ENST00000466689.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 799,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACOX2",
"gene_hgnc_id": 120,
"hgvs_c": "n.294G>T",
"hgvs_p": null,
"transcript": "ENST00000475143.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 426,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACOX2",
"gene_hgnc_id": 120,
"hgvs_c": "n.312G>T",
"hgvs_p": null,
"transcript": "ENST00000480791.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACOX2",
"gene_hgnc_id": 120,
"hgvs_c": "n.20G>T",
"hgvs_p": null,
"transcript": "ENST00000492530.1",
"protein_id": "ENSP00000419133.1",
"transcript_support_level": 3,
"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": 578,
"mane_select": null,
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACOX2",
"gene_hgnc_id": 120,
"hgvs_c": "c.-16G>T",
"hgvs_p": null,
"transcript": "XM_006713340.4",
"protein_id": "XP_006713403.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 583,
"cds_start": -4,
"cds_end": null,
"cds_length": 1752,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1927,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ACOX2",
"gene_hgnc_id": 120,
"dbsnp": "rs763287775",
"frequency_reference_population": 6.840666e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84067e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8065495491027832,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.362,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8172,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.427,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.05,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000302819.10",
"gene_symbol": "ACOX2",
"hgnc_id": 120,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.149G>T",
"hgvs_p": "p.Arg50Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}