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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: 18-63393488-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=63393488&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PP3_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "VPS4B",
"hgnc_id": 10895,
"hgvs_c": "c.1154C>T",
"hgvs_p": "p.Ser385Phe",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_004869.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS2",
"acmg_score": -2,
"allele_count_reference_population": 11,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.7383,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.32,
"chr": "18",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8672013282775879,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 444,
"aa_ref": "S",
"aa_start": 385,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3337,
"cdna_start": 1371,
"cds_end": null,
"cds_length": 1335,
"cds_start": 1154,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_004869.4",
"gene_hgnc_id": 10895,
"gene_symbol": "VPS4B",
"hgvs_c": "c.1154C>T",
"hgvs_p": "p.Ser385Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000238497.10",
"protein_coding": true,
"protein_id": "NP_004860.2",
"strand": false,
"transcript": "NM_004869.4",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 444,
"aa_ref": "S",
"aa_start": 385,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3337,
"cdna_start": 1371,
"cds_end": null,
"cds_length": 1335,
"cds_start": 1154,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000238497.10",
"gene_hgnc_id": 10895,
"gene_symbol": "VPS4B",
"hgvs_c": "c.1154C>T",
"hgvs_p": "p.Ser385Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004869.4",
"protein_coding": true,
"protein_id": "ENSP00000238497.4",
"strand": false,
"transcript": "ENST00000238497.10",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 434,
"aa_ref": "S",
"aa_start": 375,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3271,
"cdna_start": 1311,
"cds_end": null,
"cds_length": 1305,
"cds_start": 1124,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000930479.1",
"gene_hgnc_id": 10895,
"gene_symbol": "VPS4B",
"hgvs_c": "c.1124C>T",
"hgvs_p": "p.Ser375Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600538.1",
"strand": false,
"transcript": "ENST00000930479.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 404,
"aa_ref": "S",
"aa_start": 345,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3083,
"cdna_start": 1234,
"cds_end": null,
"cds_length": 1215,
"cds_start": 1034,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000930480.1",
"gene_hgnc_id": 10895,
"gene_symbol": "VPS4B",
"hgvs_c": "c.1034C>T",
"hgvs_p": "p.Ser345Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600539.1",
"strand": false,
"transcript": "ENST00000930480.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 369,
"aa_ref": "S",
"aa_start": 310,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3094,
"cdna_start": 1128,
"cds_end": null,
"cds_length": 1110,
"cds_start": 929,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000930478.1",
"gene_hgnc_id": 10895,
"gene_symbol": "VPS4B",
"hgvs_c": "c.929C>T",
"hgvs_p": "p.Ser310Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600537.1",
"strand": false,
"transcript": "ENST00000930478.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 342,
"aa_ref": "S",
"aa_start": 283,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2133,
"cdna_start": 1036,
"cds_end": null,
"cds_length": 1029,
"cds_start": 848,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000863557.1",
"gene_hgnc_id": 10895,
"gene_symbol": "VPS4B",
"hgvs_c": "c.848C>T",
"hgvs_p": "p.Ser283Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533615.1",
"strand": false,
"transcript": "ENST00000863557.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 326,
"aa_ref": "S",
"aa_start": 267,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2870,
"cdna_start": 904,
"cds_end": null,
"cds_length": 981,
"cds_start": 800,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047437949.1",
"gene_hgnc_id": 10895,
"gene_symbol": "VPS4B",
"hgvs_c": "c.800C>T",
"hgvs_p": "p.Ser267Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047293905.1",
"strand": false,
"transcript": "XM_047437949.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 397,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3193,
"cdna_start": null,
"cds_end": null,
"cds_length": 1194,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000930477.1",
"gene_hgnc_id": 10895,
"gene_symbol": "VPS4B",
"hgvs_c": "c.1093-2412C>T",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600536.1",
"strand": false,
"transcript": "ENST00000930477.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1252,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000588059.5",
"gene_hgnc_id": 10895,
"gene_symbol": "VPS4B",
"hgvs_c": "n.*668C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000465944.1",
"strand": false,
"transcript": "ENST00000588059.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 463,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000588323.1",
"gene_hgnc_id": 10895,
"gene_symbol": "VPS4B",
"hgvs_c": "n.170C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000588323.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1252,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000588059.5",
"gene_hgnc_id": 10895,
"gene_symbol": "VPS4B",
"hgvs_c": "n.*668C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000465944.1",
"strand": false,
"transcript": "ENST00000588059.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1033915095",
"effect": "missense_variant",
"frequency_reference_population": 0.000007530894,
"gene_hgnc_id": 10895,
"gene_symbol": "VPS4B",
"gnomad_exomes_ac": 11,
"gnomad_exomes_af": 0.00000753089,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.892,
"pos": 63393488,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.848,
"splice_prediction_selected": "Uncertain_significance",
"splice_score_selected": 0.2800000011920929,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Uncertain_significance",
"spliceai_max_score": 0.28,
"transcript": "NM_004869.4"
}
]
}