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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-2909935-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=2909935&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ARSD",
"hgnc_id": 717,
"hgvs_c": "c.1180G>T",
"hgvs_p": "p.Gly394Trp",
"inheritance_mode": "",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_001669.4",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_score": 6,
"allele_count_reference_population": 1,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.9629,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.25,
"chr": "X",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9692447185516357,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 593,
"aa_ref": "G",
"aa_start": 394,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5145,
"cdna_start": 1244,
"cds_end": null,
"cds_length": 1782,
"cds_start": 1180,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001669.4",
"gene_hgnc_id": 717,
"gene_symbol": "ARSD",
"hgvs_c": "c.1180G>T",
"hgvs_p": "p.Gly394Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000381154.6",
"protein_coding": true,
"protein_id": "NP_001660.2",
"strand": false,
"transcript": "NM_001669.4",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 593,
"aa_ref": "G",
"aa_start": 394,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5145,
"cdna_start": 1244,
"cds_end": null,
"cds_length": 1782,
"cds_start": 1180,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000381154.6",
"gene_hgnc_id": 717,
"gene_symbol": "ARSD",
"hgvs_c": "c.1180G>T",
"hgvs_p": "p.Gly394Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001669.4",
"protein_coding": true,
"protein_id": "ENSP00000370546.1",
"strand": false,
"transcript": "ENST00000381154.6",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 548,
"aa_ref": "G",
"aa_start": 349,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5076,
"cdna_start": 1175,
"cds_end": null,
"cds_length": 1647,
"cds_start": 1045,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000954947.1",
"gene_hgnc_id": 717,
"gene_symbol": "ARSD",
"hgvs_c": "c.1045G>T",
"hgvs_p": "p.Gly349Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625006.1",
"strand": false,
"transcript": "ENST00000954947.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 406,
"aa_ref": "G",
"aa_start": 207,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2357,
"cdna_start": 640,
"cds_end": null,
"cds_length": 1221,
"cds_start": 619,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000954949.1",
"gene_hgnc_id": 717,
"gene_symbol": "ARSD",
"hgvs_c": "c.619G>T",
"hgvs_p": "p.Gly207Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625008.1",
"strand": false,
"transcript": "ENST00000954949.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 548,
"aa_ref": "G",
"aa_start": 349,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5010,
"cdna_start": 1109,
"cds_end": null,
"cds_length": 1647,
"cds_start": 1045,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_005274514.3",
"gene_hgnc_id": 717,
"gene_symbol": "ARSD",
"hgvs_c": "c.1045G>T",
"hgvs_p": "p.Gly349Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005274571.1",
"strand": false,
"transcript": "XM_005274514.3",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 547,
"aa_ref": "G",
"aa_start": 348,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5055,
"cdna_start": 1154,
"cds_end": null,
"cds_length": 1644,
"cds_start": 1042,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_047442108.1",
"gene_hgnc_id": 717,
"gene_symbol": "ARSD",
"hgvs_c": "c.1042G>T",
"hgvs_p": "p.Gly348Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047298064.1",
"strand": false,
"transcript": "XM_047442108.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 475,
"aa_ref": "G",
"aa_start": 394,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5497,
"cdna_start": 1244,
"cds_end": null,
"cds_length": 1428,
"cds_start": 1180,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_005274515.3",
"gene_hgnc_id": 717,
"gene_symbol": "ARSD",
"hgvs_c": "c.1180G>T",
"hgvs_p": "p.Gly394Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005274572.1",
"strand": false,
"transcript": "XM_005274515.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 448,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2548,
"cdna_start": null,
"cds_end": null,
"cds_length": 1347,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000954948.1",
"gene_hgnc_id": 717,
"gene_symbol": "ARSD",
"hgvs_c": "c.864-1093G>T",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625007.1",
"strand": false,
"transcript": "ENST00000954948.1",
"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": 2032,
"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": "ENST00000495294.1",
"gene_hgnc_id": 717,
"gene_symbol": "ARSD",
"hgvs_c": "n.119-1130G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000495294.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 159,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 580,
"cdna_start": null,
"cds_end": null,
"cds_length": 480,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000458014.1",
"gene_hgnc_id": 717,
"gene_symbol": "ARSD",
"hgvs_c": "c.-15G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000409180.1",
"strand": true,
"transcript": "ENST00000458014.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs746453494",
"effect": "missense_variant",
"frequency_reference_population": 0.000009067252,
"gene_hgnc_id": 717,
"gene_symbol": "ARSD",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000906725,
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.64,
"pos": 2909935,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.658,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001669.4"
}
]
}