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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: 1-155235002-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=155235002&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 155235002,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000368373.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA1",
"gene_hgnc_id": 4177,
"hgvs_c": "c.1604G>A",
"hgvs_p": "p.Arg535His",
"transcript": "NM_000157.4",
"protein_id": "NP_000148.2",
"transcript_support_level": null,
"aa_start": 535,
"aa_end": null,
"aa_length": 536,
"cds_start": 1604,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 1741,
"cdna_end": null,
"cdna_length": 2291,
"mane_select": "ENST00000368373.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA1",
"gene_hgnc_id": 4177,
"hgvs_c": "c.1604G>A",
"hgvs_p": "p.Arg535His",
"transcript": "ENST00000368373.8",
"protein_id": "ENSP00000357357.3",
"transcript_support_level": 1,
"aa_start": 535,
"aa_end": null,
"aa_length": 536,
"cds_start": 1604,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 1741,
"cdna_end": null,
"cdna_length": 2291,
"mane_select": "NM_000157.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA1",
"gene_hgnc_id": 4177,
"hgvs_c": "c.1604G>A",
"hgvs_p": "p.Arg535His",
"transcript": "ENST00000327247.9",
"protein_id": "ENSP00000314508.5",
"transcript_support_level": 1,
"aa_start": 535,
"aa_end": null,
"aa_length": 536,
"cds_start": 1604,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 1837,
"cdna_end": null,
"cdna_length": 2387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA1",
"gene_hgnc_id": 4177,
"hgvs_c": "c.1604G>A",
"hgvs_p": "p.Arg535His",
"transcript": "NM_001005741.3",
"protein_id": "NP_001005741.1",
"transcript_support_level": null,
"aa_start": 535,
"aa_end": null,
"aa_length": 536,
"cds_start": 1604,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 1794,
"cdna_end": null,
"cdna_length": 2344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA1",
"gene_hgnc_id": 4177,
"hgvs_c": "c.1604G>A",
"hgvs_p": "p.Arg535His",
"transcript": "NM_001005742.3",
"protein_id": "NP_001005742.1",
"transcript_support_level": null,
"aa_start": 535,
"aa_end": null,
"aa_length": 536,
"cds_start": 1604,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 1775,
"cdna_end": null,
"cdna_length": 2325,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA1",
"gene_hgnc_id": 4177,
"hgvs_c": "c.1457G>A",
"hgvs_p": "p.Arg486His",
"transcript": "NM_001171812.2",
"protein_id": "NP_001165283.1",
"transcript_support_level": null,
"aa_start": 486,
"aa_end": null,
"aa_length": 487,
"cds_start": 1457,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 1594,
"cdna_end": null,
"cdna_length": 2144,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA1",
"gene_hgnc_id": 4177,
"hgvs_c": "c.1457G>A",
"hgvs_p": "p.Arg486His",
"transcript": "ENST00000427500.7",
"protein_id": "ENSP00000402577.2",
"transcript_support_level": 2,
"aa_start": 486,
"aa_end": null,
"aa_length": 487,
"cds_start": 1457,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 1620,
"cdna_end": null,
"cdna_length": 2063,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA1",
"gene_hgnc_id": 4177,
"hgvs_c": "c.1343G>A",
"hgvs_p": "p.Arg448His",
"transcript": "NM_001171811.2",
"protein_id": "NP_001165282.1",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 449,
"cds_start": 1343,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 1611,
"cdna_end": null,
"cdna_length": 2161,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA1",
"gene_hgnc_id": 4177,
"hgvs_c": "c.1343G>A",
"hgvs_p": "p.Arg448His",
"transcript": "ENST00000428024.3",
"protein_id": "ENSP00000397986.2",
"transcript_support_level": 2,
"aa_start": 448,
"aa_end": null,
"aa_length": 449,
"cds_start": 1343,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 1683,
"cdna_end": null,
"cdna_length": 1817,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA1",
"gene_hgnc_id": 4177,
"hgvs_c": "n.964G>A",
"hgvs_p": null,
"transcript": "ENST00000478472.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 1005,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GBA1",
"gene_hgnc_id": 4177,
"hgvs_c": "n.191-181G>A",
"hgvs_p": null,
"transcript": "ENST00000464536.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA1",
"gene_hgnc_id": 4177,
"hgvs_c": "n.*14G>A",
"hgvs_p": null,
"transcript": "ENST00000484489.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GBA1",
"gene_hgnc_id": 4177,
"dbsnp": "rs75822236",
"frequency_reference_population": 0.00011757478,
"hom_count_reference_population": 0,
"allele_count_reference_population": 80,
"gnomad_exomes_af": 0.000117575,
"gnomad_genomes_af": 0.0000552792,
"gnomad_exomes_ac": 80,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.32971787452697754,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.566,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1018,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.26,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.83,
"phylop100way_prediction": "Benign",
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM5,PP2,PP5_Very_Strong,BP4",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 1,
"pathogenic_score": 13,
"criteria": [
"PM1",
"PM5",
"PP2",
"PP5_Very_Strong",
"BP4"
],
"verdict": "Pathogenic",
"transcript": "ENST00000368373.8",
"gene_symbol": "GBA1",
"hgnc_id": 4177,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1604G>A",
"hgvs_p": "p.Arg535His"
}
],
"clinvar_disease": " late-onset,7 conditions,Gaucher disease,Gaucher disease type I,Gaucher disease type II,Gaucher disease type III,Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome,Parkinson disease,not provided,not specified",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:16 LP:1 O:1",
"phenotype_combined": "Gaucher disease type I|7 conditions|Gaucher disease|not provided|Gaucher disease type I;Gaucher disease type II;Gaucher disease type III;Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome|not specified|Parkinson disease, late-onset",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}