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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: 17-42541069-TC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=42541069&ref=TC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 42541069,
"ref": "TC",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "ENST00000225927.7",
"consequences": [
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.886delC",
"hgvs_p": "p.Leu296fs",
"transcript": "NM_000263.4",
"protein_id": "NP_000254.2",
"transcript_support_level": null,
"aa_start": 296,
"aa_end": null,
"aa_length": 743,
"cds_start": 886,
"cds_end": null,
"cds_length": 2232,
"cdna_start": 918,
"cdna_end": null,
"cdna_length": 2475,
"mane_select": "ENST00000225927.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.886delC",
"hgvs_p": "p.Leu296fs",
"transcript": "ENST00000225927.7",
"protein_id": "ENSP00000225927.1",
"transcript_support_level": 1,
"aa_start": 296,
"aa_end": null,
"aa_length": 743,
"cds_start": 886,
"cds_end": null,
"cds_length": 2232,
"cdna_start": 918,
"cdna_end": null,
"cdna_length": 2475,
"mane_select": "NM_000263.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_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.487delC",
"hgvs_p": "p.Leu163fs",
"transcript": "ENST00000586516.5",
"protein_id": "ENSP00000467135.1",
"transcript_support_level": 2,
"aa_start": 163,
"aa_end": null,
"aa_length": 168,
"cds_start": 487,
"cds_end": null,
"cds_length": 509,
"cdna_start": 488,
"cdna_end": null,
"cdna_length": 510,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.943delC",
"hgvs_p": "p.Leu315fs",
"transcript": "XM_024450771.2",
"protein_id": "XP_024306539.1",
"transcript_support_level": null,
"aa_start": 315,
"aa_end": null,
"aa_length": 762,
"cds_start": 943,
"cds_end": null,
"cds_length": 2289,
"cdna_start": 975,
"cdna_end": null,
"cdna_length": 2532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.277delC",
"hgvs_p": "p.Leu93fs",
"transcript": "XM_047436138.1",
"protein_id": "XP_047292094.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 540,
"cds_start": 277,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 770,
"cdna_end": null,
"cdna_length": 2327,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.55delC",
"hgvs_p": "p.Leu19fs",
"transcript": "XM_017024687.2",
"protein_id": "XP_016880176.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 466,
"cds_start": 55,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 133,
"cdna_end": null,
"cdna_length": 1690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.360-1957delC",
"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+2316delC",
"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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.23-1957delC",
"hgvs_p": null,
"transcript": "XM_047436139.1",
"protein_id": "XP_047292095.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 410,
"cds_start": -4,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"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": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"hgvs_c": "c.-22delC",
"hgvs_p": null,
"transcript": "ENST00000592454.1",
"protein_id": "ENSP00000468665.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 64,
"cds_start": -4,
"cds_end": null,
"cds_length": 195,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NAGLU",
"gene_hgnc_id": 7632,
"dbsnp": "rs752131463",
"frequency_reference_population": 0.0000020521325,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205213,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 2.472,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000225927.7",
"gene_symbol": "NAGLU",
"hgnc_id": 7632,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.886delC",
"hgvs_p": "p.Leu296fs"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000585572.1",
"gene_symbol": "ENSG00000266929",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.379+2316delC",
"hgvs_p": null
}
],
"clinvar_disease": " MPS-III-B,Charcot-Marie-Tooth disease axonal type 2V,Inborn genetic diseases,Mucopolysaccharidosis",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"phenotype_combined": "Inborn genetic diseases|Mucopolysaccharidosis, MPS-III-B;Charcot-Marie-Tooth disease axonal type 2V",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}