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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: 17-42544026-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=42544026&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 42544026,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000225927.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.2020C>T",
"hgvs_p": "p.Arg674Cys",
"transcript": "NM_000263.4",
"protein_id": "NP_000254.2",
"transcript_support_level": null,
"aa_start": 674,
"aa_end": null,
"aa_length": 743,
"cds_start": 2020,
"cds_end": null,
"cds_length": 2232,
"cdna_start": 2052,
"cdna_end": null,
"cdna_length": 2475,
"mane_select": "ENST00000225927.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.2020C>T",
"hgvs_p": "p.Arg674Cys",
"transcript": "ENST00000225927.7",
"protein_id": "ENSP00000225927.1",
"transcript_support_level": 1,
"aa_start": 674,
"aa_end": null,
"aa_length": 743,
"cds_start": 2020,
"cds_end": null,
"cds_length": 2232,
"cdna_start": 2052,
"cdna_end": null,
"cdna_length": 2475,
"mane_select": "NM_000263.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.2077C>T",
"hgvs_p": "p.Arg693Cys",
"transcript": "XM_024450771.2",
"protein_id": "XP_024306539.1",
"transcript_support_level": null,
"aa_start": 693,
"aa_end": null,
"aa_length": 762,
"cds_start": 2077,
"cds_end": null,
"cds_length": 2289,
"cdna_start": 2109,
"cdna_end": null,
"cdna_length": 2532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.1411C>T",
"hgvs_p": "p.Arg471Cys",
"transcript": "XM_047436138.1",
"protein_id": "XP_047292094.1",
"transcript_support_level": null,
"aa_start": 471,
"aa_end": null,
"aa_length": 540,
"cds_start": 1411,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1904,
"cdna_end": null,
"cdna_length": 2327,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.1189C>T",
"hgvs_p": "p.Arg397Cys",
"transcript": "XM_017024687.2",
"protein_id": "XP_016880176.1",
"transcript_support_level": null,
"aa_start": 397,
"aa_end": null,
"aa_length": 466,
"cds_start": 1189,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 1267,
"cdna_end": null,
"cdna_length": 1690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.1021C>T",
"hgvs_p": "p.Arg341Cys",
"transcript": "XM_047436139.1",
"protein_id": "XP_047292095.1",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 410,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 1099,
"cdna_end": null,
"cdna_length": 1522,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.*989C>T",
"hgvs_p": null,
"transcript": "ENST00000591587.1",
"protein_id": "ENSP00000467836.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 122,
"cds_start": -4,
"cds_end": null,
"cds_length": 369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1493,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000266929",
"gene_hgnc_id": null,
"hgvs_c": "n.379+5271C>T",
"hgvs_p": null,
"transcript": "ENST00000585572.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"dbsnp": "rs763299645",
"frequency_reference_population": 0.00001675701,
"hom_count_reference_population": 0,
"allele_count_reference_population": 27,
"gnomad_exomes_af": 0.0000164483,
"gnomad_genomes_af": 0.0000197174,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.995286226272583,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.956,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6916,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.57,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.845,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM1",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000225927.7",
"gene_symbol": "NAGLU",
"hgnc_id": 7632,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2020C>T",
"hgvs_p": "p.Arg674Cys"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000585572.1",
"gene_symbol": "ENSG00000266929",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.379+5271C>T",
"hgvs_p": null
}
],
"clinvar_disease": " MPS-III-B,Charcot-Marie-Tooth disease axonal type 2V,Mucopolysaccharidosis,Tip-toe gait,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:3",
"phenotype_combined": "Mucopolysaccharidosis, MPS-III-B|Tip-toe gait|not provided|Charcot-Marie-Tooth disease axonal type 2V;Mucopolysaccharidosis, MPS-III-B",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}