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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: 8-11758419-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=11758419&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 11758419,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000532059.6",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA4",
"gene_hgnc_id": 4173,
"hgvs_c": "c.1276G>A",
"hgvs_p": "p.Asp426Asn",
"transcript": "NM_001308093.3",
"protein_id": "NP_001295022.1",
"transcript_support_level": null,
"aa_start": 426,
"aa_end": null,
"aa_length": 443,
"cds_start": 1276,
"cds_end": null,
"cds_length": 1332,
"cdna_start": 1836,
"cdna_end": null,
"cdna_length": 3419,
"mane_select": "ENST00000532059.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA4",
"gene_hgnc_id": 4173,
"hgvs_c": "c.1276G>A",
"hgvs_p": "p.Asp426Asn",
"transcript": "ENST00000532059.6",
"protein_id": "ENSP00000435712.1",
"transcript_support_level": 1,
"aa_start": 426,
"aa_end": null,
"aa_length": 443,
"cds_start": 1276,
"cds_end": null,
"cds_length": 1332,
"cdna_start": 1836,
"cdna_end": null,
"cdna_length": 3419,
"mane_select": "NM_001308093.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA4",
"gene_hgnc_id": 4173,
"hgvs_c": "c.1273G>A",
"hgvs_p": "p.Asp425Asn",
"transcript": "NM_002052.5",
"protein_id": "NP_002043.2",
"transcript_support_level": null,
"aa_start": 425,
"aa_end": null,
"aa_length": 442,
"cds_start": 1273,
"cds_end": null,
"cds_length": 1329,
"cdna_start": 1833,
"cdna_end": null,
"cdna_length": 3416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA4",
"gene_hgnc_id": 4173,
"hgvs_c": "c.1273G>A",
"hgvs_p": "p.Asp425Asn",
"transcript": "ENST00000335135.8",
"protein_id": "ENSP00000334458.4",
"transcript_support_level": 5,
"aa_start": 425,
"aa_end": null,
"aa_length": 442,
"cds_start": 1273,
"cds_end": null,
"cds_length": 1329,
"cdna_start": 1831,
"cdna_end": null,
"cdna_length": 3414,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA4",
"gene_hgnc_id": 4173,
"hgvs_c": "c.1273G>A",
"hgvs_p": "p.Asp425Asn",
"transcript": "ENST00000622443.3",
"protein_id": "ENSP00000482268.2",
"transcript_support_level": 5,
"aa_start": 425,
"aa_end": null,
"aa_length": 442,
"cds_start": 1273,
"cds_end": null,
"cds_length": 1329,
"cdna_start": 1933,
"cdna_end": null,
"cdna_length": 3508,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA4",
"gene_hgnc_id": 4173,
"hgvs_c": "c.655G>A",
"hgvs_p": "p.Asp219Asn",
"transcript": "NM_001308094.2",
"protein_id": "NP_001295023.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 236,
"cds_start": 655,
"cds_end": null,
"cds_length": 711,
"cdna_start": 1057,
"cdna_end": null,
"cdna_length": 2640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA4",
"gene_hgnc_id": 4173,
"hgvs_c": "c.655G>A",
"hgvs_p": "p.Asp219Asn",
"transcript": "NM_001374273.1",
"protein_id": "NP_001361202.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 236,
"cds_start": 655,
"cds_end": null,
"cds_length": 711,
"cdna_start": 760,
"cdna_end": null,
"cdna_length": 2343,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA4",
"gene_hgnc_id": 4173,
"hgvs_c": "c.655G>A",
"hgvs_p": "p.Asp219Asn",
"transcript": "ENST00000528712.5",
"protein_id": "ENSP00000435043.1",
"transcript_support_level": 2,
"aa_start": 219,
"aa_end": null,
"aa_length": 236,
"cds_start": 655,
"cds_end": null,
"cds_length": 711,
"cdna_start": 1033,
"cdna_end": null,
"cdna_length": 2614,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA4",
"gene_hgnc_id": 4173,
"hgvs_c": "c.529G>A",
"hgvs_p": "p.Asp177Asn",
"transcript": "NM_001374274.1",
"protein_id": "NP_001361203.1",
"transcript_support_level": null,
"aa_start": 177,
"aa_end": null,
"aa_length": 194,
"cds_start": 529,
"cds_end": null,
"cds_length": 585,
"cdna_start": 793,
"cdna_end": null,
"cdna_length": 2376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA4",
"gene_hgnc_id": 4173,
"hgvs_c": "n.718G>A",
"hgvs_p": null,
"transcript": "ENST00000526021.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1064,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GATA4",
"gene_hgnc_id": 4173,
"dbsnp": "rs56208331",
"frequency_reference_population": 0.0009620865,
"hom_count_reference_population": 16,
"allele_count_reference_population": 1553,
"gnomad_exomes_af": 0.000996666,
"gnomad_genomes_af": 0.000630227,
"gnomad_exomes_ac": 1457,
"gnomad_genomes_ac": 96,
"gnomad_exomes_homalt": 16,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00697559118270874,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.742,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.194,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.497,
"phylop100way_prediction": "Pathogenic",
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000532059.6",
"gene_symbol": "GATA4",
"hgnc_id": 4173,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1276G>A",
"hgvs_p": "p.Asp426Asn"
}
],
"clinvar_disease": "Atrial septal defect 2,Atrioventricular septal defect 4,Congenital heart disease,GATA4-related disorder,Inborn genetic diseases,Pulmonary valve atresia,Pulmonic stenosis,Testicular anomalies with or without congenital heart disease,Tetralogy of Fallot,Tricuspid regurgitation,Ventricular septal defect 1,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:2 B:4",
"phenotype_combined": "Atrial septal defect 2|Tetralogy of Fallot|Pulmonic stenosis;Tricuspid regurgitation;Pulmonary valve atresia|Inborn genetic diseases|not specified|not provided|Atrioventricular septal defect 4|GATA4-related disorder|Congenital heart disease|Ventricular septal defect 1;Atrioventricular septal defect 4;Testicular anomalies with or without congenital heart disease;Tetralogy of Fallot;Atrial septal defect 2",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}