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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-17725820-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=17725820&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NHS",
"hgnc_id": 7820,
"hgvs_c": "c.1714C>T",
"hgvs_p": "p.Pro572Ser",
"inheritance_mode": "XL,AD",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_001291867.2",
"verdict": "Benign"
},
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000309710",
"hgnc_id": null,
"hgvs_c": "n.299+7781G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -20,
"transcript": "ENST00000843253.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_score": -20,
"allele_count_reference_population": 26449,
"alphamissense_prediction": null,
"alphamissense_score": 0.2223,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.34,
"chr": "X",
"clinvar_classification": "Benign",
"clinvar_disease": "Inborn genetic diseases,Nance-Horan syndrome,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0016627013683319092,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1651,
"aa_ref": "P",
"aa_start": 572,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9044,
"cdna_start": 2272,
"cds_end": null,
"cds_length": 4956,
"cds_start": 1714,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001291867.2",
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"hgvs_c": "c.1714C>T",
"hgvs_p": "p.Pro572Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000676302.1",
"protein_coding": true,
"protein_id": "NP_001278796.1",
"strand": true,
"transcript": "NM_001291867.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1651,
"aa_ref": "P",
"aa_start": 572,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9044,
"cdna_start": 2272,
"cds_end": null,
"cds_length": 4956,
"cds_start": 1714,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000676302.1",
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"hgvs_c": "c.1714C>T",
"hgvs_p": "p.Pro572Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001291867.2",
"protein_coding": true,
"protein_id": "ENSP00000502262.1",
"strand": true,
"transcript": "ENST00000676302.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1630,
"aa_ref": "P",
"aa_start": 551,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8761,
"cdna_start": 1989,
"cds_end": null,
"cds_length": 4893,
"cds_start": 1651,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000380060.7",
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"hgvs_c": "c.1651C>T",
"hgvs_p": "p.Pro551Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000369400.3",
"strand": true,
"transcript": "ENST00000380060.7",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1474,
"aa_ref": "P",
"aa_start": 395,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8213,
"cdna_start": 1457,
"cds_end": null,
"cds_length": 4425,
"cds_start": 1183,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000398097.7",
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"hgvs_c": "c.1183C>T",
"hgvs_p": "p.Pro395Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000381170.3",
"strand": true,
"transcript": "ENST00000398097.7",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1447,
"aa_ref": "P",
"aa_start": 368,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8163,
"cdna_start": 1394,
"cds_end": null,
"cds_length": 4344,
"cds_start": 1102,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000617601.4",
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"hgvs_c": "c.1102C>T",
"hgvs_p": "p.Pro368Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000478433.1",
"strand": true,
"transcript": "ENST00000617601.4",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1630,
"aa_ref": "P",
"aa_start": 551,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8981,
"cdna_start": 2209,
"cds_end": null,
"cds_length": 4893,
"cds_start": 1651,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_198270.4",
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"hgvs_c": "c.1651C>T",
"hgvs_p": "p.Pro551Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_938011.1",
"strand": true,
"transcript": "NM_198270.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1538,
"aa_ref": "P",
"aa_start": 459,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8202,
"cdna_start": 1430,
"cds_end": null,
"cds_length": 4617,
"cds_start": 1375,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001440780.1",
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"hgvs_c": "c.1375C>T",
"hgvs_p": "p.Pro459Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001427709.1",
"strand": true,
"transcript": "NM_001440780.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1474,
"aa_ref": "P",
"aa_start": 395,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8022,
"cdna_start": 1250,
"cds_end": null,
"cds_length": 4425,
"cds_start": 1183,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001136024.4",
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"hgvs_c": "c.1183C>T",
"hgvs_p": "p.Pro395Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001129496.1",
"strand": true,
"transcript": "NM_001136024.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1453,
"aa_ref": "P",
"aa_start": 374,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7959,
"cdna_start": 1187,
"cds_end": null,
"cds_length": 4362,
"cds_start": 1120,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001291868.2",
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"hgvs_c": "c.1120C>T",
"hgvs_p": "p.Pro374Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001278797.1",
"strand": true,
"transcript": "NM_001291868.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1335,
"aa_ref": "P",
"aa_start": 256,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7701,
"cdna_start": 929,
"cds_end": null,
"cds_length": 4008,
"cds_start": 766,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_011545528.3",
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"hgvs_c": "c.766C>T",
"hgvs_p": "p.Pro256Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011543830.1",
"strand": true,
"transcript": "XM_011545528.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 8865,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000615422.2",
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"hgvs_c": "n.2109C>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": "ENST00000615422.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3704,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000690213.1",
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"hgvs_c": "n.3594C>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": "ENST00000690213.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3877,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000690608.1",
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"hgvs_c": "n.671C>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": "ENST00000690608.1",
"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": 602,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000843253.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000309710",
"hgvs_c": "n.299+7781G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000843253.1",
"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": 640,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000843254.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000309710",
"hgvs_c": "n.260-5718G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000843254.1",
"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": 352,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000843255.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000309710",
"hgvs_c": "n.260-5718G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000843255.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs150688899",
"effect": "missense_variant",
"frequency_reference_population": 0.021869414,
"gene_hgnc_id": 7820,
"gene_symbol": "NHS",
"gnomad_exomes_ac": 19630,
"gnomad_exomes_af": 0.0178745,
"gnomad_exomes_homalt": 475,
"gnomad_genomes_ac": 6819,
"gnomad_genomes_af": 0.0613247,
"gnomad_genomes_homalt": 413,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 8809,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|Nance-Horan syndrome|not provided|Inborn genetic diseases",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.856,
"pos": 17725820,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.249,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001291867.2"
}
]
}