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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: 9-132264841-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=132264841&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 132264841,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001351528.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7432A>G",
"hgvs_p": "p.Thr2478Ala",
"transcript": "NM_015046.7",
"protein_id": "NP_055861.3",
"transcript_support_level": null,
"aa_start": 2478,
"aa_end": null,
"aa_length": 2677,
"cds_start": 7432,
"cds_end": null,
"cds_length": 8034,
"cdna_start": 7616,
"cdna_end": null,
"cdna_length": 11101,
"mane_select": "ENST00000224140.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015046.7"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7432A>G",
"hgvs_p": "p.Thr2478Ala",
"transcript": "ENST00000224140.6",
"protein_id": "ENSP00000224140.5",
"transcript_support_level": 1,
"aa_start": 2478,
"aa_end": null,
"aa_length": 2677,
"cds_start": 7432,
"cds_end": null,
"cds_length": 8034,
"cdna_start": 7616,
"cdna_end": null,
"cdna_length": 11101,
"mane_select": "NM_015046.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000224140.6"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7558A>G",
"hgvs_p": "p.Thr2520Ala",
"transcript": "ENST00000923216.1",
"protein_id": "ENSP00000593275.1",
"transcript_support_level": null,
"aa_start": 2520,
"aa_end": null,
"aa_length": 2719,
"cds_start": 7558,
"cds_end": null,
"cds_length": 8160,
"cdna_start": 7742,
"cdna_end": null,
"cdna_length": 11143,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923216.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7519A>G",
"hgvs_p": "p.Thr2507Ala",
"transcript": "NM_001351528.2",
"protein_id": "NP_001338457.1",
"transcript_support_level": null,
"aa_start": 2507,
"aa_end": null,
"aa_length": 2706,
"cds_start": 7519,
"cds_end": null,
"cds_length": 8121,
"cdna_start": 7703,
"cdna_end": null,
"cdna_length": 11188,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001351528.2"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7471A>G",
"hgvs_p": "p.Thr2491Ala",
"transcript": "ENST00000923217.1",
"protein_id": "ENSP00000593276.1",
"transcript_support_level": null,
"aa_start": 2491,
"aa_end": null,
"aa_length": 2690,
"cds_start": 7471,
"cds_end": null,
"cds_length": 8073,
"cdna_start": 7655,
"cdna_end": null,
"cdna_length": 11056,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923217.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7432A>G",
"hgvs_p": "p.Thr2478Ala",
"transcript": "NM_001351527.2",
"protein_id": "NP_001338456.1",
"transcript_support_level": null,
"aa_start": 2478,
"aa_end": null,
"aa_length": 2677,
"cds_start": 7432,
"cds_end": null,
"cds_length": 8034,
"cdna_start": 7752,
"cdna_end": null,
"cdna_length": 11237,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001351527.2"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7432A>G",
"hgvs_p": "p.Thr2478Ala",
"transcript": "ENST00000905306.1",
"protein_id": "ENSP00000575365.1",
"transcript_support_level": null,
"aa_start": 2478,
"aa_end": null,
"aa_length": 2677,
"cds_start": 7432,
"cds_end": null,
"cds_length": 8034,
"cdna_start": 7944,
"cdna_end": null,
"cdna_length": 8889,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905306.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7432A>G",
"hgvs_p": "p.Thr2478Ala",
"transcript": "ENST00000923215.1",
"protein_id": "ENSP00000593274.1",
"transcript_support_level": null,
"aa_start": 2478,
"aa_end": null,
"aa_length": 2677,
"cds_start": 7432,
"cds_end": null,
"cds_length": 8034,
"cdna_start": 7904,
"cdna_end": null,
"cdna_length": 11305,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923215.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7405A>G",
"hgvs_p": "p.Thr2469Ala",
"transcript": "ENST00000923219.1",
"protein_id": "ENSP00000593278.1",
"transcript_support_level": null,
"aa_start": 2469,
"aa_end": null,
"aa_length": 2668,
"cds_start": 7405,
"cds_end": null,
"cds_length": 8007,
"cdna_start": 7591,
"cdna_end": null,
"cdna_length": 8539,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923219.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7366A>G",
"hgvs_p": "p.Thr2456Ala",
"transcript": "ENST00000947394.1",
"protein_id": "ENSP00000617453.1",
"transcript_support_level": null,
"aa_start": 2456,
"aa_end": null,
"aa_length": 2655,
"cds_start": 7366,
"cds_end": null,
"cds_length": 7968,
"cdna_start": 7527,
"cdna_end": null,
"cdna_length": 9667,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947394.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.3451A>G",
"hgvs_p": "p.Thr1151Ala",
"transcript": "ENST00000923218.1",
"protein_id": "ENSP00000593277.1",
"transcript_support_level": null,
"aa_start": 1151,
"aa_end": null,
"aa_length": 1350,
"cds_start": 3451,
"cds_end": null,
"cds_length": 4053,
"cdna_start": 3628,
"cdna_end": null,
"cdna_length": 7026,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923218.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.3256A>G",
"hgvs_p": "p.Thr1086Ala",
"transcript": "ENST00000905305.1",
"protein_id": "ENSP00000575364.1",
"transcript_support_level": null,
"aa_start": 1086,
"aa_end": null,
"aa_length": 1285,
"cds_start": 3256,
"cds_end": null,
"cds_length": 3858,
"cdna_start": 3442,
"cdna_end": null,
"cdna_length": 4463,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905305.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"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": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.2245A>G",
"hgvs_p": "p.Thr749Ala",
"transcript": "ENST00000436441.5",
"protein_id": "ENSP00000409143.1",
"transcript_support_level": 5,
"aa_start": 749,
"aa_end": null,
"aa_length": 948,
"cds_start": 2245,
"cds_end": null,
"cds_length": 2847,
"cdna_start": 2245,
"cdna_end": null,
"cdna_length": 5730,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000436441.5"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7519A>G",
"hgvs_p": "p.Thr2507Ala",
"transcript": "XM_005272172.4",
"protein_id": "XP_005272229.1",
"transcript_support_level": null,
"aa_start": 2507,
"aa_end": null,
"aa_length": 2706,
"cds_start": 7519,
"cds_end": null,
"cds_length": 8121,
"cdna_start": 7819,
"cdna_end": null,
"cdna_length": 11304,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005272172.4"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7519A>G",
"hgvs_p": "p.Thr2507Ala",
"transcript": "XM_005272173.4",
"protein_id": "XP_005272230.1",
"transcript_support_level": null,
"aa_start": 2507,
"aa_end": null,
"aa_length": 2706,
"cds_start": 7519,
"cds_end": null,
"cds_length": 8121,
"cdna_start": 7839,
"cdna_end": null,
"cdna_length": 11324,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005272173.4"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7519A>G",
"hgvs_p": "p.Thr2507Ala",
"transcript": "XM_011518404.4",
"protein_id": "XP_011516706.1",
"transcript_support_level": null,
"aa_start": 2507,
"aa_end": null,
"aa_length": 2706,
"cds_start": 7519,
"cds_end": null,
"cds_length": 8121,
"cdna_start": 7848,
"cdna_end": null,
"cdna_length": 11333,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011518404.4"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7519A>G",
"hgvs_p": "p.Thr2507Ala",
"transcript": "XM_011518405.4",
"protein_id": "XP_011516707.1",
"transcript_support_level": null,
"aa_start": 2507,
"aa_end": null,
"aa_length": 2706,
"cds_start": 7519,
"cds_end": null,
"cds_length": 8121,
"cdna_start": 7983,
"cdna_end": null,
"cdna_length": 11468,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011518405.4"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7432A>G",
"hgvs_p": "p.Thr2478Ala",
"transcript": "XM_047423023.1",
"protein_id": "XP_047278979.1",
"transcript_support_level": null,
"aa_start": 2478,
"aa_end": null,
"aa_length": 2677,
"cds_start": 7432,
"cds_end": null,
"cds_length": 8034,
"cdna_start": 7896,
"cdna_end": null,
"cdna_length": 11381,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423023.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "n.582A>G",
"hgvs_p": null,
"transcript": "ENST00000477049.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4067,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000477049.1"
}
],
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"dbsnp": "rs142303658",
"frequency_reference_population": 0.00019329537,
"hom_count_reference_population": 1,
"allele_count_reference_population": 312,
"gnomad_exomes_af": 0.000179907,
"gnomad_genomes_af": 0.000321848,
"gnomad_exomes_ac": 263,
"gnomad_genomes_ac": 49,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.011653423309326172,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.195,
"revel_prediction": "Benign",
"alphamissense_score": 0.0548,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.518,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NM_001351528.2",
"gene_symbol": "SETX",
"hgnc_id": 445,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.7519A>G",
"hgvs_p": "p.Thr2507Ala"
}
],
"clinvar_disease": " autosomal recessive, with axonal neuropathy 2,Amyotrophic lateral sclerosis type 4,Inborn genetic diseases,SETX-related disorder,Spinocerebellar ataxia,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:4 B:1",
"phenotype_combined": "not specified|Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2;Amyotrophic lateral sclerosis type 4|Inborn genetic diseases|not provided|Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2|SETX-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}