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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: 5-180313899-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=180313899&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GFPT2",
"hgnc_id": 4242,
"hgvs_c": "c.1339G>A",
"hgvs_p": "p.Val447Ile",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_005110.4",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "ENSG00000297119",
"hgnc_id": null,
"hgvs_c": "n.-19C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -4,
"transcript": "ENST00000745608.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 21,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.052,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.59,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.06563317775726318,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 682,
"aa_ref": "V",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3034,
"cdna_start": 1458,
"cds_end": null,
"cds_length": 2049,
"cds_start": 1339,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_005110.4",
"gene_hgnc_id": 4242,
"gene_symbol": "GFPT2",
"hgvs_c": "c.1339G>A",
"hgvs_p": "p.Val447Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000253778.13",
"protein_coding": true,
"protein_id": "NP_005101.1",
"strand": false,
"transcript": "NM_005110.4",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 682,
"aa_ref": "V",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3034,
"cdna_start": 1458,
"cds_end": null,
"cds_length": 2049,
"cds_start": 1339,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000253778.13",
"gene_hgnc_id": 4242,
"gene_symbol": "GFPT2",
"hgvs_c": "c.1339G>A",
"hgvs_p": "p.Val447Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005110.4",
"protein_coding": true,
"protein_id": "ENSP00000253778.8",
"strand": false,
"transcript": "ENST00000253778.13",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 703,
"aa_ref": "V",
"aa_start": 468,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3099,
"cdna_start": 1524,
"cds_end": null,
"cds_length": 2112,
"cds_start": 1402,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000889627.1",
"gene_hgnc_id": 4242,
"gene_symbol": "GFPT2",
"hgvs_c": "c.1402G>A",
"hgvs_p": "p.Val468Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559686.1",
"strand": false,
"transcript": "ENST00000889627.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 681,
"aa_ref": "V",
"aa_start": 446,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3034,
"cdna_start": 1458,
"cds_end": null,
"cds_length": 2046,
"cds_start": 1336,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000920229.1",
"gene_hgnc_id": 4242,
"gene_symbol": "GFPT2",
"hgvs_c": "c.1336G>A",
"hgvs_p": "p.Val446Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590288.1",
"strand": false,
"transcript": "ENST00000920229.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 646,
"aa_ref": "V",
"aa_start": 411,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2932,
"cdna_start": 1353,
"cds_end": null,
"cds_length": 1941,
"cds_start": 1231,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000920227.1",
"gene_hgnc_id": 4242,
"gene_symbol": "GFPT2",
"hgvs_c": "c.1231G>A",
"hgvs_p": "p.Val411Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590286.1",
"strand": false,
"transcript": "ENST00000920227.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 628,
"aa_ref": "V",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2888,
"cdna_start": 1461,
"cds_end": null,
"cds_length": 1887,
"cds_start": 1339,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000889625.1",
"gene_hgnc_id": 4242,
"gene_symbol": "GFPT2",
"hgvs_c": "c.1339G>A",
"hgvs_p": "p.Val447Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559684.1",
"strand": false,
"transcript": "ENST00000889625.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 627,
"aa_ref": "V",
"aa_start": 446,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2867,
"cdna_start": 1454,
"cds_end": null,
"cds_length": 1884,
"cds_start": 1336,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000953748.1",
"gene_hgnc_id": 4242,
"gene_symbol": "GFPT2",
"hgvs_c": "c.1336G>A",
"hgvs_p": "p.Val446Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000623807.1",
"strand": false,
"transcript": "ENST00000953748.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 626,
"aa_ref": "V",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2868,
"cdna_start": 1461,
"cds_end": null,
"cds_length": 1881,
"cds_start": 1339,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000889626.1",
"gene_hgnc_id": 4242,
"gene_symbol": "GFPT2",
"hgvs_c": "c.1339G>A",
"hgvs_p": "p.Val447Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559685.1",
"strand": false,
"transcript": "ENST00000889626.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 607,
"aa_ref": "V",
"aa_start": 372,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2813,
"cdna_start": 1236,
"cds_end": null,
"cds_length": 1824,
"cds_start": 1114,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000920228.1",
"gene_hgnc_id": 4242,
"gene_symbol": "GFPT2",
"hgvs_c": "c.1114G>A",
"hgvs_p": "p.Val372Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590287.1",
"strand": false,
"transcript": "ENST00000920228.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 572,
"aa_ref": "V",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2723,
"cdna_start": 1461,
"cds_end": null,
"cds_length": 1719,
"cds_start": 1339,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000920226.1",
"gene_hgnc_id": 4242,
"gene_symbol": "GFPT2",
"hgvs_c": "c.1339G>A",
"hgvs_p": "p.Val447Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590285.1",
"strand": false,
"transcript": "ENST00000920226.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 591,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2760,
"cdna_start": null,
"cds_end": null,
"cds_length": 1776,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000920230.1",
"gene_hgnc_id": 4242,
"gene_symbol": "GFPT2",
"hgvs_c": "c.1273+2442G>A",
"hgvs_p": null,
"intron_rank": 13,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590289.1",
"strand": false,
"transcript": "ENST00000920230.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 589,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2755,
"cdna_start": null,
"cds_end": null,
"cds_length": 1770,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000953747.1",
"gene_hgnc_id": 4242,
"gene_symbol": "GFPT2",
"hgvs_c": "c.1153-1355G>A",
"hgvs_p": null,
"intron_rank": 12,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000623806.1",
"strand": false,
"transcript": "ENST00000953747.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 586,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000745608.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000297119",
"hgvs_c": "n.-19C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000745608.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1012796939",
"effect": "missense_variant",
"frequency_reference_population": 0.000013070545,
"gene_hgnc_id": 4242,
"gene_symbol": "GFPT2",
"gnomad_exomes_ac": 13,
"gnomad_exomes_af": 0.00000893782,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 8,
"gnomad_genomes_af": 0.0000525721,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.169,
"pos": 180313899,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.023,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005110.4"
}
]
}