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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: 18-63400087-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=63400087&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 63400087,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004869.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"hgvs_c": "c.751G>A",
"hgvs_p": "p.Ala251Thr",
"transcript": "NM_004869.4",
"protein_id": "NP_004860.2",
"transcript_support_level": null,
"aa_start": 251,
"aa_end": null,
"aa_length": 444,
"cds_start": 751,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000238497.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004869.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"hgvs_c": "c.751G>A",
"hgvs_p": "p.Ala251Thr",
"transcript": "ENST00000238497.10",
"protein_id": "ENSP00000238497.4",
"transcript_support_level": 1,
"aa_start": 251,
"aa_end": null,
"aa_length": 444,
"cds_start": 751,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004869.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000238497.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"hgvs_c": "n.887G>A",
"hgvs_p": null,
"transcript": "ENST00000589604.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000589604.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"hgvs_c": "n.975G>A",
"hgvs_p": null,
"transcript": "ENST00000591475.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000591475.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr",
"transcript": "ENST00000930479.1",
"protein_id": "ENSP00000600538.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 434,
"cds_start": 721,
"cds_end": null,
"cds_length": 1305,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930479.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"hgvs_c": "c.631G>A",
"hgvs_p": "p.Ala211Thr",
"transcript": "ENST00000930480.1",
"protein_id": "ENSP00000600539.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 404,
"cds_start": 631,
"cds_end": null,
"cds_length": 1215,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930480.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"hgvs_c": "c.751G>A",
"hgvs_p": "p.Ala251Thr",
"transcript": "ENST00000930477.1",
"protein_id": "ENSP00000600536.1",
"transcript_support_level": null,
"aa_start": 251,
"aa_end": null,
"aa_length": 397,
"cds_start": 751,
"cds_end": null,
"cds_length": 1194,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930477.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"hgvs_c": "c.526G>A",
"hgvs_p": "p.Ala176Thr",
"transcript": "ENST00000930478.1",
"protein_id": "ENSP00000600537.1",
"transcript_support_level": null,
"aa_start": 176,
"aa_end": null,
"aa_length": 369,
"cds_start": 526,
"cds_end": null,
"cds_length": 1110,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930478.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Ala133Thr",
"transcript": "XM_047437949.1",
"protein_id": "XP_047293905.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 326,
"cds_start": 397,
"cds_end": null,
"cds_length": 981,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437949.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"hgvs_c": "c.485-764G>A",
"hgvs_p": null,
"transcript": "ENST00000863557.1",
"protein_id": "ENSP00000533615.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 342,
"cds_start": null,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000863557.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"hgvs_c": "n.*347G>A",
"hgvs_p": null,
"transcript": "ENST00000588059.5",
"protein_id": "ENSP00000465944.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000588059.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"hgvs_c": "n.593G>A",
"hgvs_p": null,
"transcript": "ENST00000591383.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000591383.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"hgvs_c": "n.*347G>A",
"hgvs_p": null,
"transcript": "ENST00000588059.5",
"protein_id": "ENSP00000465944.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000588059.5"
}
],
"gene_symbol": "VPS4B",
"gene_hgnc_id": 10895,
"dbsnp": "rs138933226",
"frequency_reference_population": 0.000047147514,
"hom_count_reference_population": 0,
"allele_count_reference_population": 76,
"gnomad_exomes_af": 0.0000458949,
"gnomad_genomes_af": 0.0000591693,
"gnomad_exomes_ac": 67,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.43975192308425903,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.538,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7669,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.12,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.879,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_004869.4",
"gene_symbol": "VPS4B",
"hgnc_id": 10895,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.751G>A",
"hgvs_p": "p.Ala251Thr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}