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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: X-149482974-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=149482974&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "IDS",
"hgnc_id": 5389,
"hgvs_c": "c.1425G>A",
"hgvs_p": "p.Trp475*",
"inheritance_mode": "XL",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_000202.8",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "ENSG00000241489",
"hgnc_id": null,
"hgvs_c": "c.792G>A",
"hgvs_p": "p.Trp264*",
"inheritance_mode": "",
"pathogenic_score": 18,
"score": 18,
"transcript": "ENST00000651111.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.54,
"chr": "X",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": " MPS-II,Mucopolysaccharidosis",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.5400000214576721,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 550,
"aa_ref": "W",
"aa_start": 475,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7580,
"cdna_start": 1594,
"cds_end": null,
"cds_length": 1653,
"cds_start": 1425,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_000202.8",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1425G>A",
"hgvs_p": "p.Trp475*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000340855.11",
"protein_coding": true,
"protein_id": "NP_000193.1",
"strand": false,
"transcript": "NM_000202.8",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 550,
"aa_ref": "W",
"aa_start": 475,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7580,
"cdna_start": 1594,
"cds_end": null,
"cds_length": 1653,
"cds_start": 1425,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000340855.11",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1425G>A",
"hgvs_p": "p.Trp475*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000202.8",
"protein_coding": true,
"protein_id": "ENSP00000339801.6",
"strand": false,
"transcript": "ENST00000340855.11",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 339,
"aa_ref": "W",
"aa_start": 264,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9159,
"cdna_start": 3289,
"cds_end": null,
"cds_length": 1020,
"cds_start": 792,
"consequences": [
"stop_gained"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000651111.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000241489",
"hgvs_c": "c.792G>A",
"hgvs_p": "p.Trp264*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000498395.1",
"strand": false,
"transcript": "ENST00000651111.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 577,
"aa_ref": "W",
"aa_start": 502,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2139,
"cdna_start": 1708,
"cds_end": null,
"cds_length": 1734,
"cds_start": 1506,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000875674.1",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1506G>A",
"hgvs_p": "p.Trp502*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545733.1",
"strand": false,
"transcript": "ENST00000875674.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 570,
"aa_ref": "W",
"aa_start": 495,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2419,
"cdna_start": 1651,
"cds_end": null,
"cds_length": 1713,
"cds_start": 1485,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000875673.1",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1485G>A",
"hgvs_p": "p.Trp495*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545732.1",
"strand": false,
"transcript": "ENST00000875673.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 565,
"aa_ref": "W",
"aa_start": 490,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5125,
"cdna_start": 1675,
"cds_end": null,
"cds_length": 1698,
"cds_start": 1470,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000875670.1",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1470G>A",
"hgvs_p": "p.Trp490*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545729.1",
"strand": false,
"transcript": "ENST00000875670.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 565,
"aa_ref": "W",
"aa_start": 490,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5858,
"cdna_start": 1654,
"cds_end": null,
"cds_length": 1698,
"cds_start": 1470,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000947400.1",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1470G>A",
"hgvs_p": "p.Trp490*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617459.1",
"strand": false,
"transcript": "ENST00000947400.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 547,
"aa_ref": "W",
"aa_start": 472,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2353,
"cdna_start": 1585,
"cds_end": null,
"cds_length": 1644,
"cds_start": 1416,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000875672.1",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1416G>A",
"hgvs_p": "p.Trp472*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545731.1",
"strand": false,
"transcript": "ENST00000875672.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 512,
"aa_ref": "W",
"aa_start": 437,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1866,
"cdna_start": 1437,
"cds_end": null,
"cds_length": 1539,
"cds_start": 1311,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000947401.1",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1311G>A",
"hgvs_p": "p.Trp437*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617460.1",
"strand": false,
"transcript": "ENST00000947401.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 507,
"aa_ref": "W",
"aa_start": 432,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5427,
"cdna_start": 1461,
"cds_end": null,
"cds_length": 1524,
"cds_start": 1296,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000875668.1",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1296G>A",
"hgvs_p": "p.Trp432*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545727.1",
"strand": false,
"transcript": "ENST00000875668.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 503,
"aa_ref": "W",
"aa_start": 428,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5004,
"cdna_start": 1401,
"cds_end": null,
"cds_length": 1512,
"cds_start": 1284,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000875669.1",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1284G>A",
"hgvs_p": "p.Trp428*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545728.1",
"strand": false,
"transcript": "ENST00000875669.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 492,
"aa_ref": "W",
"aa_start": 417,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5673,
"cdna_start": 1468,
"cds_end": null,
"cds_length": 1479,
"cds_start": 1251,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000875667.1",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1251G>A",
"hgvs_p": "p.Trp417*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545726.1",
"strand": false,
"transcript": "ENST00000875667.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 483,
"aa_ref": "W",
"aa_start": 408,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4881,
"cdna_start": 1432,
"cds_end": null,
"cds_length": 1452,
"cds_start": 1224,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000930297.1",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1224G>A",
"hgvs_p": "p.Trp408*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600356.1",
"strand": false,
"transcript": "ENST00000930297.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 480,
"aa_ref": "W",
"aa_start": 405,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4842,
"cdna_start": 1383,
"cds_end": null,
"cds_length": 1443,
"cds_start": 1215,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000930298.1",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1215G>A",
"hgvs_p": "p.Trp405*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600357.1",
"strand": false,
"transcript": "ENST00000930298.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 460,
"aa_ref": "W",
"aa_start": 385,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7536,
"cdna_start": 1550,
"cds_end": null,
"cds_length": 1383,
"cds_start": 1155,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001166550.4",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1155G>A",
"hgvs_p": "p.Trp385*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001160022.1",
"strand": false,
"transcript": "NM_001166550.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 445,
"aa_ref": "W",
"aa_start": 370,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4757,
"cdna_start": 1300,
"cds_end": null,
"cds_length": 1338,
"cds_start": 1110,
"consequences": [
"stop_gained"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000875671.1",
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"hgvs_c": "c.1110G>A",
"hgvs_p": "p.Trp370*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545730.1",
"strand": false,
"transcript": "ENST00000875671.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 339,
"aa_ref": "W",
"aa_start": 264,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2635,
"cdna_start": 2204,
"cds_end": null,
"cds_length": 1020,
"cds_start": 792,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000422081.6",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000241489",
"hgvs_c": "c.792G>A",
"hgvs_p": "p.Trp264*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000477056.1",
"strand": false,
"transcript": "ENST00000422081.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 416,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000441880.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000241489",
"hgvs_c": "n.*116G>A",
"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": "ENST00000441880.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs199422230",
"effect": "stop_gained",
"frequency_reference_population": null,
"gene_hgnc_id": 5389,
"gene_symbol": "IDS",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"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": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Mucopolysaccharidosis, MPS-II",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.067,
"pos": 149482974,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000202.8"
}
]
}