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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: 17-58307630-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=58307630&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 58307630,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004758.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPOAP1",
"gene_hgnc_id": 16831,
"hgvs_c": "c.4964G>A",
"hgvs_p": "p.Arg1655Gln",
"transcript": "NM_004758.4",
"protein_id": "NP_004749.2",
"transcript_support_level": null,
"aa_start": 1655,
"aa_end": null,
"aa_length": 1857,
"cds_start": 4964,
"cds_end": null,
"cds_length": 5574,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000343736.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004758.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPOAP1",
"gene_hgnc_id": 16831,
"hgvs_c": "c.4964G>A",
"hgvs_p": "p.Arg1655Gln",
"transcript": "ENST00000343736.9",
"protein_id": "ENSP00000345824.4",
"transcript_support_level": 1,
"aa_start": 1655,
"aa_end": null,
"aa_length": 1857,
"cds_start": 4964,
"cds_end": null,
"cds_length": 5574,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004758.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000343736.9"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPOAP1",
"gene_hgnc_id": 16831,
"hgvs_c": "c.4784G>A",
"hgvs_p": "p.Arg1595Gln",
"transcript": "ENST00000268893.10",
"protein_id": "ENSP00000268893.6",
"transcript_support_level": 1,
"aa_start": 1595,
"aa_end": null,
"aa_length": 1797,
"cds_start": 4784,
"cds_end": null,
"cds_length": 5394,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000268893.10"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPOAP1",
"gene_hgnc_id": 16831,
"hgvs_c": "c.4964G>A",
"hgvs_p": "p.Arg1655Gln",
"transcript": "NM_001261835.2",
"protein_id": "NP_001248764.1",
"transcript_support_level": null,
"aa_start": 1655,
"aa_end": null,
"aa_length": 1848,
"cds_start": 4964,
"cds_end": null,
"cds_length": 5547,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001261835.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPOAP1",
"gene_hgnc_id": 16831,
"hgvs_c": "c.4784G>A",
"hgvs_p": "p.Arg1595Gln",
"transcript": "NM_024418.3",
"protein_id": "NP_077729.1",
"transcript_support_level": null,
"aa_start": 1595,
"aa_end": null,
"aa_length": 1797,
"cds_start": 4784,
"cds_end": null,
"cds_length": 5394,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024418.3"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPOAP1",
"gene_hgnc_id": 16831,
"hgvs_c": "c.2360G>A",
"hgvs_p": "p.Arg787Gln",
"transcript": "ENST00000580669.6",
"protein_id": "ENSP00000462822.2",
"transcript_support_level": 5,
"aa_start": 787,
"aa_end": null,
"aa_length": 980,
"cds_start": 2360,
"cds_end": null,
"cds_length": 2943,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000580669.6"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPOAP1",
"gene_hgnc_id": 16831,
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Arg218Gln",
"transcript": "ENST00000582679.1",
"protein_id": "ENSP00000462710.1",
"transcript_support_level": 5,
"aa_start": 218,
"aa_end": null,
"aa_length": 294,
"cds_start": 653,
"cds_end": null,
"cds_length": 886,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000582679.1"
},
{
"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": "TSPOAP1",
"gene_hgnc_id": 16831,
"hgvs_c": "n.284G>A",
"hgvs_p": null,
"transcript": "ENST00000578486.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000578486.1"
}
],
"gene_symbol": "TSPOAP1",
"gene_hgnc_id": 16831,
"dbsnp": "rs147089668",
"frequency_reference_population": 0.0013587748,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2193,
"gnomad_exomes_af": 0.0014012,
"gnomad_genomes_af": 0.000951768,
"gnomad_exomes_ac": 2048,
"gnomad_genomes_ac": 145,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.010245561599731445,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.044,
"revel_prediction": "Benign",
"alphamissense_score": 0.07,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.27,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_004758.4",
"gene_symbol": "TSPOAP1",
"hgnc_id": 16831,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4964G>A",
"hgvs_p": "p.Arg1655Gln"
}
],
"clinvar_disease": "TSPOAP1-related Dystonia,TSPOAP1-related disorder,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "TSPOAP1-related Dystonia|not specified|TSPOAP1-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}