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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: 7-99768458-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=99768458&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 99768458,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000651514.1",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP3A4",
"gene_hgnc_id": 2637,
"hgvs_c": "c.566T>C",
"hgvs_p": "p.Phe189Ser",
"transcript": "NM_017460.6",
"protein_id": "NP_059488.2",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 503,
"cds_start": 566,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 669,
"cdna_end": null,
"cdna_length": 2781,
"mane_select": "ENST00000651514.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP3A4",
"gene_hgnc_id": 2637,
"hgvs_c": "c.566T>C",
"hgvs_p": "p.Phe189Ser",
"transcript": "ENST00000651514.1",
"protein_id": "ENSP00000498939.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 503,
"cds_start": 566,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 669,
"cdna_end": null,
"cdna_length": 2781,
"mane_select": "NM_017460.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP3A4",
"gene_hgnc_id": 2637,
"hgvs_c": "c.566T>C",
"hgvs_p": "p.Phe189Ser",
"transcript": "ENST00000336411.7",
"protein_id": "ENSP00000337915.3",
"transcript_support_level": 1,
"aa_start": 189,
"aa_end": null,
"aa_length": 534,
"cds_start": 566,
"cds_end": null,
"cds_length": 1605,
"cdna_start": 669,
"cdna_end": null,
"cdna_length": 2165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP3A4",
"gene_hgnc_id": 2637,
"hgvs_c": "c.566T>C",
"hgvs_p": "p.Phe189Ser",
"transcript": "NM_001202855.3",
"protein_id": "NP_001189784.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 502,
"cds_start": 566,
"cds_end": null,
"cds_length": 1509,
"cdna_start": 669,
"cdna_end": null,
"cdna_length": 2778,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP3A4",
"gene_hgnc_id": 2637,
"hgvs_c": "c.419T>C",
"hgvs_p": "p.Phe140Ser",
"transcript": "ENST00000652018.1",
"protein_id": "ENSP00000498733.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 454,
"cds_start": 419,
"cds_end": null,
"cds_length": 1365,
"cdna_start": 586,
"cdna_end": null,
"cdna_length": 1982,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP3A4",
"gene_hgnc_id": 2637,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Phe39Ser",
"transcript": "ENST00000354593.6",
"protein_id": "ENSP00000346607.2",
"transcript_support_level": 5,
"aa_start": 39,
"aa_end": null,
"aa_length": 353,
"cds_start": 116,
"cds_end": null,
"cds_length": 1062,
"cdna_start": 223,
"cdna_end": null,
"cdna_length": 2342,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CYP3A4",
"gene_hgnc_id": 2637,
"dbsnp": "rs4987161",
"frequency_reference_population": 0.0000099130375,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.00000889347,
"gnomad_genomes_af": 0.0000196993,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8973597884178162,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.8,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9349,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.39,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.735,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000651514.1",
"gene_symbol": "CYP3A4",
"hgnc_id": 2637,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AD",
"hgvs_c": "c.566T>C",
"hgvs_p": "p.Phe189Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}