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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: 5-146339166-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=146339166&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 146339166,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001414499.1",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POU4F3",
"gene_hgnc_id": 9220,
"hgvs_c": "c.54A>C",
"hgvs_p": "p.Glu18Asp",
"transcript": "NM_002700.3",
"protein_id": "NP_002691.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 338,
"cds_start": 54,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000646991.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002700.3"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POU4F3",
"gene_hgnc_id": 9220,
"hgvs_c": "c.54A>C",
"hgvs_p": "p.Glu18Asp",
"transcript": "ENST00000646991.2",
"protein_id": "ENSP00000495718.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 338,
"cds_start": 54,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002700.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000646991.2"
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000275740",
"gene_hgnc_id": 58349,
"hgvs_c": "c.3010A>C",
"hgvs_p": "p.Thr1004Pro",
"transcript": "ENST00000506502.2",
"protein_id": "ENSP00000475384.1",
"transcript_support_level": 5,
"aa_start": 1004,
"aa_end": null,
"aa_length": 1027,
"cds_start": 3010,
"cds_end": null,
"cds_length": 3084,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000506502.2"
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RBM27-POU4F3",
"gene_hgnc_id": 58349,
"hgvs_c": "c.2887A>C",
"hgvs_p": "p.Thr963Pro",
"transcript": "NM_001414499.1",
"protein_id": "NP_001401428.1",
"transcript_support_level": null,
"aa_start": 963,
"aa_end": null,
"aa_length": 987,
"cds_start": 2887,
"cds_end": null,
"cds_length": 2964,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001414499.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POU4F3",
"gene_hgnc_id": 9220,
"hgvs_c": "c.54A>C",
"hgvs_p": "p.Glu18Asp",
"transcript": "ENST00000914229.1",
"protein_id": "ENSP00000584288.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 338,
"cds_start": 54,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914229.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000250025",
"gene_hgnc_id": null,
"hgvs_c": "n.404-31890T>G",
"hgvs_p": null,
"transcript": "ENST00000515598.1",
"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": "pseudogene",
"feature": "ENST00000515598.1"
}
],
"gene_symbol": "RBM27-POU4F3",
"gene_hgnc_id": 58349,
"dbsnp": "rs898774220",
"frequency_reference_population": 0.000004788322,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000478832,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.22278058528900146,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.182,
"revel_prediction": "Benign",
"alphamissense_score": 0.0788,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.31,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001414499.1",
"gene_symbol": "RBM27-POU4F3",
"hgnc_id": 58349,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2887A>C",
"hgvs_p": "p.Thr963Pro"
},
{
"score": -6,
"benign_score": 7,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Moderate",
"BS1_Supporting",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_002700.3",
"gene_symbol": "POU4F3",
"hgnc_id": 9220,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.54A>C",
"hgvs_p": "p.Glu18Asp"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000506502.2",
"gene_symbol": "ENSG00000275740",
"hgnc_id": 58349,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.3010A>C",
"hgvs_p": "p.Thr1004Pro"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000515598.1",
"gene_symbol": "ENSG00000250025",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.404-31890T>G",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,POU4F3-related disorder",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Inborn genetic diseases|POU4F3-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}