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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: 9-35737405-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=35737405&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 35737405,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000378103.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.2548C>T",
"hgvs_p": "p.Arg850Cys",
"transcript": "NM_020944.3",
"protein_id": "NP_065995.1",
"transcript_support_level": null,
"aa_start": 850,
"aa_end": null,
"aa_length": 927,
"cds_start": 2548,
"cds_end": null,
"cds_length": 2784,
"cdna_start": 3072,
"cdna_end": null,
"cdna_length": 3611,
"mane_select": "ENST00000378103.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.2548C>T",
"hgvs_p": "p.Arg850Cys",
"transcript": "ENST00000378103.7",
"protein_id": "ENSP00000367343.3",
"transcript_support_level": 1,
"aa_start": 850,
"aa_end": null,
"aa_length": 927,
"cds_start": 2548,
"cds_end": null,
"cds_length": 2784,
"cdna_start": 3072,
"cdna_end": null,
"cdna_length": 3611,
"mane_select": "NM_020944.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.*71C>T",
"hgvs_p": null,
"transcript": "ENST00000378094.4",
"protein_id": "ENSP00000367334.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 877,
"cds_start": -4,
"cds_end": null,
"cds_length": 2634,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.2566C>T",
"hgvs_p": "p.Arg856Cys",
"transcript": "XM_006716809.5",
"protein_id": "XP_006716872.1",
"transcript_support_level": null,
"aa_start": 856,
"aa_end": null,
"aa_length": 933,
"cds_start": 2566,
"cds_end": null,
"cds_length": 2802,
"cdna_start": 3090,
"cdna_end": null,
"cdna_length": 3629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.2500C>T",
"hgvs_p": "p.Arg834Cys",
"transcript": "XM_005251526.6",
"protein_id": "XP_005251583.1",
"transcript_support_level": null,
"aa_start": 834,
"aa_end": null,
"aa_length": 911,
"cds_start": 2500,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 3024,
"cdna_end": null,
"cdna_length": 3563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.2482C>T",
"hgvs_p": "p.Arg828Cys",
"transcript": "XM_017014937.3",
"protein_id": "XP_016870426.1",
"transcript_support_level": null,
"aa_start": 828,
"aa_end": null,
"aa_length": 905,
"cds_start": 2482,
"cds_end": null,
"cds_length": 2718,
"cdna_start": 3006,
"cdna_end": null,
"cdna_length": 3545,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.2329C>T",
"hgvs_p": "p.Arg777Cys",
"transcript": "XM_017014940.3",
"protein_id": "XP_016870429.1",
"transcript_support_level": null,
"aa_start": 777,
"aa_end": null,
"aa_length": 854,
"cds_start": 2329,
"cds_end": null,
"cds_length": 2565,
"cdna_start": 2853,
"cdna_end": null,
"cdna_length": 3392,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.2113C>T",
"hgvs_p": "p.Arg705Cys",
"transcript": "XM_017014942.3",
"protein_id": "XP_016870431.1",
"transcript_support_level": null,
"aa_start": 705,
"aa_end": null,
"aa_length": 782,
"cds_start": 2113,
"cds_end": null,
"cds_length": 2349,
"cdna_start": 2204,
"cdna_end": null,
"cdna_length": 2743,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.2095C>T",
"hgvs_p": "p.Arg699Cys",
"transcript": "XM_017014943.3",
"protein_id": "XP_016870432.1",
"transcript_support_level": null,
"aa_start": 699,
"aa_end": null,
"aa_length": 776,
"cds_start": 2095,
"cds_end": null,
"cds_length": 2331,
"cdna_start": 2186,
"cdna_end": null,
"cdna_length": 2725,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.2011C>T",
"hgvs_p": "p.Arg671Cys",
"transcript": "XM_017014944.1",
"protein_id": "XP_016870433.1",
"transcript_support_level": null,
"aa_start": 671,
"aa_end": null,
"aa_length": 748,
"cds_start": 2011,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 2135,
"cdna_end": null,
"cdna_length": 2674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.1993C>T",
"hgvs_p": "p.Arg665Cys",
"transcript": "XM_017014945.1",
"protein_id": "XP_016870434.1",
"transcript_support_level": null,
"aa_start": 665,
"aa_end": null,
"aa_length": 742,
"cds_start": 1993,
"cds_end": null,
"cds_length": 2229,
"cdna_start": 2117,
"cdna_end": null,
"cdna_length": 2656,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.1993C>T",
"hgvs_p": "p.Arg665Cys",
"transcript": "XM_047423612.1",
"protein_id": "XP_047279568.1",
"transcript_support_level": null,
"aa_start": 665,
"aa_end": null,
"aa_length": 742,
"cds_start": 1993,
"cds_end": null,
"cds_length": 2229,
"cdna_start": 2215,
"cdna_end": null,
"cdna_length": 2754,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.*71C>T",
"hgvs_p": null,
"transcript": "NM_001330660.2",
"protein_id": "NP_001317589.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 877,
"cds_start": -4,
"cds_end": null,
"cds_length": 2634,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3768,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.*232C>T",
"hgvs_p": null,
"transcript": "ENST00000378088.1",
"protein_id": "ENSP00000367328.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 172,
"cds_start": -4,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1672,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.*71C>T",
"hgvs_p": null,
"transcript": "XM_017014938.3",
"protein_id": "XP_016870427.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 883,
"cds_start": -4,
"cds_end": null,
"cds_length": 2652,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.*71C>T",
"hgvs_p": null,
"transcript": "XM_017014939.3",
"protein_id": "XP_016870428.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 855,
"cds_start": -4,
"cds_end": null,
"cds_length": 2568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3702,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"hgvs_c": "c.*71C>T",
"hgvs_p": null,
"transcript": "XM_017014941.3",
"protein_id": "XP_016870430.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 804,
"cds_start": -4,
"cds_end": null,
"cds_length": 2415,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GBA2",
"gene_hgnc_id": 18986,
"dbsnp": "rs752274637",
"frequency_reference_population": 0.000010261799,
"hom_count_reference_population": 0,
"allele_count_reference_population": 15,
"gnomad_exomes_af": 0.0000102618,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8592473268508911,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.402,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1552,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.37,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.359,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000378103.7",
"gene_symbol": "GBA2",
"hgnc_id": 18986,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2548C>T",
"hgvs_p": "p.Arg850Cys"
}
],
"clinvar_disease": "Hereditary spastic paraplegia 46,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"phenotype_combined": "not provided|Hereditary spastic paraplegia 46",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}