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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: 17-42543342-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=42543342&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NAGLU",
"hgnc_id": 7632,
"hgvs_c": "c.1336G>A",
"hgvs_p": "p.Glu446Lys",
"inheritance_mode": "AD,AR",
"pathogenic_score": 22,
"score": 22,
"transcript": "NM_000263.4",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000266929",
"hgnc_id": null,
"hgvs_c": "n.379+4587G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 18,
"score": 18,
"transcript": "ENST00000585572.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_score": 22,
"allele_count_reference_population": 5,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.8973,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.6,
"chr": "17",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": " MPS-III-B,Charcot-Marie-Tooth disease axonal type 2V,Mucopolysaccharidosis,Mucopolysaccharidosistype IIIB",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9949509501457214,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 743,
"aa_ref": "E",
"aa_start": 446,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2475,
"cdna_start": 1368,
"cds_end": null,
"cds_length": 2232,
"cds_start": 1336,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_000263.4",
"gene_hgnc_id": 7632,
"gene_symbol": "NAGLU",
"hgvs_c": "c.1336G>A",
"hgvs_p": "p.Glu446Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000225927.7",
"protein_coding": true,
"protein_id": "NP_000254.2",
"strand": true,
"transcript": "NM_000263.4",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 743,
"aa_ref": "E",
"aa_start": 446,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2475,
"cdna_start": 1368,
"cds_end": null,
"cds_length": 2232,
"cds_start": 1336,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000225927.7",
"gene_hgnc_id": 7632,
"gene_symbol": "NAGLU",
"hgvs_c": "c.1336G>A",
"hgvs_p": "p.Glu446Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000263.4",
"protein_coding": true,
"protein_id": "ENSP00000225927.1",
"strand": true,
"transcript": "ENST00000225927.7",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 769,
"aa_ref": "E",
"aa_start": 472,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2548,
"cdna_start": 1444,
"cds_end": null,
"cds_length": 2310,
"cds_start": 1414,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000963429.1",
"gene_hgnc_id": 7632,
"gene_symbol": "NAGLU",
"hgvs_c": "c.1414G>A",
"hgvs_p": "p.Glu472Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633488.1",
"strand": true,
"transcript": "ENST00000963429.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 762,
"aa_ref": "E",
"aa_start": 465,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2530,
"cdna_start": 1425,
"cds_end": null,
"cds_length": 2289,
"cds_start": 1393,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000904921.1",
"gene_hgnc_id": 7632,
"gene_symbol": "NAGLU",
"hgvs_c": "c.1393G>A",
"hgvs_p": "p.Glu465Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574980.1",
"strand": true,
"transcript": "ENST00000904921.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 737,
"aa_ref": "E",
"aa_start": 440,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2439,
"cdna_start": 1332,
"cds_end": null,
"cds_length": 2214,
"cds_start": 1318,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000933285.1",
"gene_hgnc_id": 7632,
"gene_symbol": "NAGLU",
"hgvs_c": "c.1318G>A",
"hgvs_p": "p.Glu440Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603344.1",
"strand": true,
"transcript": "ENST00000933285.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 762,
"aa_ref": "E",
"aa_start": 465,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2532,
"cdna_start": 1425,
"cds_end": null,
"cds_length": 2289,
"cds_start": 1393,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_024450771.2",
"gene_hgnc_id": 7632,
"gene_symbol": "NAGLU",
"hgvs_c": "c.1393G>A",
"hgvs_p": "p.Glu465Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024306539.1",
"strand": true,
"transcript": "XM_024450771.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 540,
"aa_ref": "E",
"aa_start": 243,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2327,
"cdna_start": 1220,
"cds_end": null,
"cds_length": 1623,
"cds_start": 727,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_047436138.1",
"gene_hgnc_id": 7632,
"gene_symbol": "NAGLU",
"hgvs_c": "c.727G>A",
"hgvs_p": "p.Glu243Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292094.1",
"strand": true,
"transcript": "XM_047436138.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 466,
"aa_ref": "E",
"aa_start": 169,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1690,
"cdna_start": 583,
"cds_end": null,
"cds_length": 1401,
"cds_start": 505,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017024687.2",
"gene_hgnc_id": 7632,
"gene_symbol": "NAGLU",
"hgvs_c": "c.505G>A",
"hgvs_p": "p.Glu169Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016880176.1",
"strand": true,
"transcript": "XM_017024687.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 410,
"aa_ref": "E",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1522,
"cdna_start": 415,
"cds_end": null,
"cds_length": 1233,
"cds_start": 337,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047436139.1",
"gene_hgnc_id": 7632,
"gene_symbol": "NAGLU",
"hgvs_c": "c.337G>A",
"hgvs_p": "p.Glu113Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292095.1",
"strand": true,
"transcript": "XM_047436139.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 122,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1493,
"cdna_start": null,
"cds_end": null,
"cds_length": 369,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000591587.1",
"gene_hgnc_id": 7632,
"gene_symbol": "NAGLU",
"hgvs_c": "c.*305G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000467836.1",
"strand": true,
"transcript": "ENST00000591587.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 64,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 582,
"cdna_start": null,
"cds_end": null,
"cds_length": 195,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000592454.1",
"gene_hgnc_id": 7632,
"gene_symbol": "NAGLU",
"hgvs_c": "c.*179G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000468665.1",
"strand": true,
"transcript": "ENST00000592454.1",
"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": 594,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000585572.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000266929",
"hgvs_c": "n.379+4587G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000585572.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs114625063",
"effect": "missense_variant",
"frequency_reference_population": 0.0000034229133,
"gene_hgnc_id": 7632,
"gene_symbol": "NAGLU",
"gnomad_exomes_ac": 5,
"gnomad_exomes_af": 0.00000342291,
"gnomad_exomes_homalt": 0,
"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-III-B|Mucopolysaccharidosistype IIIB|Mucopolysaccharidosis, MPS-III-B;Charcot-Marie-Tooth disease axonal type 2V",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.864,
"pos": 42543342,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.957,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000263.4"
}
]
}