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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: 9-132327035-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=132327035&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 132327035,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000224140.6",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "NM_015046.7",
"protein_id": "NP_055861.3",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 2677,
"cds_start": 4563,
"cds_end": null,
"cds_length": 8034,
"cdna_start": 4747,
"cdna_end": null,
"cdna_length": 11101,
"mane_select": "ENST00000224140.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "ENST00000224140.6",
"protein_id": "ENSP00000224140.5",
"transcript_support_level": 1,
"aa_start": 1521,
"aa_end": null,
"aa_length": 2677,
"cds_start": 4563,
"cds_end": null,
"cds_length": 8034,
"cdna_start": 4747,
"cdna_end": null,
"cdna_length": 11101,
"mane_select": "NM_015046.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "NM_001351528.2",
"protein_id": "NP_001338457.1",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 2706,
"cds_start": 4563,
"cds_end": null,
"cds_length": 8121,
"cdna_start": 4747,
"cdna_end": null,
"cdna_length": 11188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "NM_001351527.2",
"protein_id": "NP_001338456.1",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 2677,
"cds_start": 4563,
"cds_end": null,
"cds_length": 8034,
"cdna_start": 4883,
"cdna_end": null,
"cdna_length": 11237,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "XM_005272172.4",
"protein_id": "XP_005272229.1",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 2706,
"cds_start": 4563,
"cds_end": null,
"cds_length": 8121,
"cdna_start": 4863,
"cdna_end": null,
"cdna_length": 11304,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "XM_005272173.4",
"protein_id": "XP_005272230.1",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 2706,
"cds_start": 4563,
"cds_end": null,
"cds_length": 8121,
"cdna_start": 4883,
"cdna_end": null,
"cdna_length": 11324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "XM_011518404.4",
"protein_id": "XP_011516706.1",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 2706,
"cds_start": 4563,
"cds_end": null,
"cds_length": 8121,
"cdna_start": 4892,
"cdna_end": null,
"cdna_length": 11333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "XM_011518405.4",
"protein_id": "XP_011516707.1",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 2706,
"cds_start": 4563,
"cds_end": null,
"cds_length": 8121,
"cdna_start": 5027,
"cdna_end": null,
"cdna_length": 11468,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "XM_047423023.1",
"protein_id": "XP_047278979.1",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 2677,
"cds_start": 4563,
"cds_end": null,
"cds_length": 8034,
"cdna_start": 5027,
"cdna_end": null,
"cdna_length": 11381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "XM_011518406.3",
"protein_id": "XP_011516708.1",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 2413,
"cds_start": 4563,
"cds_end": null,
"cds_length": 7242,
"cdna_start": 4747,
"cdna_end": null,
"cdna_length": 8220,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "XM_011518407.2",
"protein_id": "XP_011516709.1",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 2372,
"cds_start": 4563,
"cds_end": null,
"cds_length": 7119,
"cdna_start": 4747,
"cdna_end": null,
"cdna_length": 9962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "XM_011518408.4",
"protein_id": "XP_011516710.1",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 2191,
"cds_start": 4563,
"cds_end": null,
"cds_length": 6576,
"cdna_start": 4747,
"cdna_end": null,
"cdna_length": 6883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "XM_047423024.1",
"protein_id": "XP_047278980.1",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 1695,
"cds_start": 4563,
"cds_end": null,
"cds_length": 5088,
"cdna_start": 4747,
"cdna_end": null,
"cdna_length": 5290,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu",
"transcript": "XM_047423025.1",
"protein_id": "XP_047278981.1",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 1558,
"cds_start": 4563,
"cds_end": null,
"cds_length": 4677,
"cdna_start": 4747,
"cdna_end": null,
"cdna_length": 4929,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"dbsnp": "rs374149839",
"frequency_reference_population": 0.000032215936,
"hom_count_reference_population": 0,
"allele_count_reference_population": 52,
"gnomad_exomes_af": 0.0000342027,
"gnomad_genomes_af": 0.0000131377,
"gnomad_exomes_ac": 50,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8500000238418579,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.85,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.006,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000224140.6",
"gene_symbol": "SETX",
"hgnc_id": 445,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.4563A>G",
"hgvs_p": "p.Glu1521Glu"
}
],
"clinvar_disease": " autosomal recessive, with axonal neuropathy 2,Amyotrophic lateral sclerosis type 4,Inborn genetic diseases,SETX-related disorder,Spinocerebellar ataxia",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4",
"phenotype_combined": "Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2;Amyotrophic lateral sclerosis type 4|Inborn genetic diseases|Amyotrophic lateral sclerosis type 4|Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2|SETX-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}