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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: 4-2462871-CG-TC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=2462871&ref=CG&alt=TC&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [],
"effects": [
"missense_variant"
],
"gene_symbol": "CFAP99",
"hgnc_id": 51180,
"hgvs_c": "c.1886_1887delCGinsTC",
"hgvs_p": "p.Ala629Val",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_001193282.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [],
"effects": [
"intron_variant"
],
"gene_symbol": "RNF4",
"hgnc_id": 10067,
"hgvs_c": "c.-158+266_-158+267delCGinsTC",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": 0,
"transcript": "ENST00000503659.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "LOC105374353",
"hgnc_id": null,
"hgvs_c": "n.-138_-137delCGinsTC",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": 0,
"transcript": "XR_925057.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_score": 0,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "TC",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "4",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 646,
"aa_ref": "A",
"aa_start": 629,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2173,
"cdna_start": 2042,
"cds_end": null,
"cds_length": 1941,
"cds_start": 1886,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001193282.4",
"gene_hgnc_id": 51180,
"gene_symbol": "CFAP99",
"hgvs_c": "c.1886_1887delCGinsTC",
"hgvs_p": "p.Ala629Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000635017.2",
"protein_coding": true,
"protein_id": "NP_001180211.2",
"strand": true,
"transcript": "NM_001193282.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 646,
"aa_ref": "A",
"aa_start": 629,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2173,
"cdna_start": 2042,
"cds_end": null,
"cds_length": 1941,
"cds_start": 1886,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000635017.2",
"gene_hgnc_id": 51180,
"gene_symbol": "CFAP99",
"hgvs_c": "c.1886_1887delCGinsTC",
"hgvs_p": "p.Ala629Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001193282.4",
"protein_coding": true,
"protein_id": "ENSP00000488922.2",
"strand": true,
"transcript": "ENST00000635017.2",
"transcript_support_level": 5
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 647,
"aa_ref": "A",
"aa_start": 630,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2177,
"cdna_start": 2045,
"cds_end": null,
"cds_length": 1944,
"cds_start": 1889,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000860043.1",
"gene_hgnc_id": 51180,
"gene_symbol": "CFAP99",
"hgvs_c": "c.1889_1890delCGinsTC",
"hgvs_p": "p.Ala630Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530102.1",
"strand": true,
"transcript": "ENST00000860043.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 714,
"aa_ref": "A",
"aa_start": 697,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2301,
"cdna_start": 2246,
"cds_end": null,
"cds_length": 2145,
"cds_start": 2090,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047415685.1",
"gene_hgnc_id": 51180,
"gene_symbol": "CFAP99",
"hgvs_c": "c.2090_2091delCGinsTC",
"hgvs_p": "p.Ala697Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271641.1",
"strand": true,
"transcript": "XM_047415685.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 4,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 558,
"cdna_start": null,
"cds_end": null,
"cds_length": 15,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000503659.5",
"gene_hgnc_id": 10067,
"gene_symbol": "RNF4",
"hgvs_c": "c.-158+266_-158+267delCGinsTC",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423186.1",
"strand": true,
"transcript": "ENST00000503659.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1389,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007057992.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC105374353",
"hgvs_c": "n.-133_-132delCGinsTC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007057992.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1276,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_925057.3",
"gene_hgnc_id": null,
"gene_symbol": "LOC105374353",
"hgvs_c": "n.-138_-137delCGinsTC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_925057.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 51180,
"gene_symbol": "CFAP99",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.27,
"pos": 2462871,
"ref": "CG",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_001193282.4"
}
]
}