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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: 22-41152194-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=41152194&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "EP300",
"hgnc_id": 3373,
"hgvs_c": "c.2998-12G>A",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_001429.4",
"verdict": "Benign"
},
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "EP300-AS1",
"hgnc_id": 50504,
"hgvs_c": "n.358-10603C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -13,
"transcript": "ENST00000717631.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_score": -13,
"allele_count_reference_population": 2296,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.82,
"chr": "22",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Rubinstein-Taybi syndrome due to EP300 haploinsufficiency,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8199999928474426,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2414,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8779,
"cdna_start": null,
"cds_end": null,
"cds_length": 7245,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001429.4",
"gene_hgnc_id": 3373,
"gene_symbol": "EP300",
"hgvs_c": "c.2998-12G>A",
"hgvs_p": null,
"intron_rank": 15,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000263253.9",
"protein_coding": true,
"protein_id": "NP_001420.2",
"strand": true,
"transcript": "NM_001429.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2414,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8779,
"cdna_start": null,
"cds_end": null,
"cds_length": 7245,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000263253.9",
"gene_hgnc_id": 3373,
"gene_symbol": "EP300",
"hgvs_c": "c.2998-12G>A",
"hgvs_p": null,
"intron_rank": 15,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001429.4",
"protein_coding": true,
"protein_id": "ENSP00000263253.7",
"strand": true,
"transcript": "ENST00000263253.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2424,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9582,
"cdna_start": null,
"cds_end": null,
"cds_length": 7275,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000916082.1",
"gene_hgnc_id": 3373,
"gene_symbol": "EP300",
"hgvs_c": "c.2998-12G>A",
"hgvs_p": null,
"intron_rank": 15,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586141.1",
"strand": true,
"transcript": "ENST00000916082.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2414,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8859,
"cdna_start": null,
"cds_end": null,
"cds_length": 7245,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000715703.1",
"gene_hgnc_id": 3373,
"gene_symbol": "EP300",
"hgvs_c": "c.2998-12G>A",
"hgvs_p": null,
"intron_rank": 15,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000520505.1",
"strand": true,
"transcript": "ENST00000715703.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2398,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9066,
"cdna_start": null,
"cds_end": null,
"cds_length": 7197,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 30,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000916084.1",
"gene_hgnc_id": 3373,
"gene_symbol": "EP300",
"hgvs_c": "c.2920-12G>A",
"hgvs_p": null,
"intron_rank": 14,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586143.1",
"strand": true,
"transcript": "ENST00000916084.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2388,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8701,
"cdna_start": null,
"cds_end": null,
"cds_length": 7167,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 30,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001362843.2",
"gene_hgnc_id": 3373,
"gene_symbol": "EP300",
"hgvs_c": "c.2920-12G>A",
"hgvs_p": null,
"intron_rank": 14,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001349772.1",
"strand": true,
"transcript": "NM_001362843.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2388,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8288,
"cdna_start": null,
"cds_end": null,
"cds_length": 7167,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 30,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000674155.1",
"gene_hgnc_id": 3373,
"gene_symbol": "EP300",
"hgvs_c": "c.2920-12G>A",
"hgvs_p": null,
"intron_rank": 14,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501078.1",
"strand": true,
"transcript": "ENST00000674155.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2383,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9457,
"cdna_start": null,
"cds_end": null,
"cds_length": 7152,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 30,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000916083.1",
"gene_hgnc_id": 3373,
"gene_symbol": "EP300",
"hgvs_c": "c.2905-12G>A",
"hgvs_p": null,
"intron_rank": 14,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586142.1",
"strand": true,
"transcript": "ENST00000916083.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5256,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 30,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000703544.1",
"gene_hgnc_id": 3373,
"gene_symbol": "EP300",
"hgvs_c": "n.*918-12G>A",
"hgvs_p": null,
"intron_rank": 14,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000515365.1",
"strand": true,
"transcript": "ENST00000703544.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3378,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000703545.1",
"gene_hgnc_id": 3373,
"gene_symbol": "EP300",
"hgvs_c": "n.*1368-12G>A",
"hgvs_p": null,
"intron_rank": 13,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000515366.1",
"strand": true,
"transcript": "ENST00000703545.1",
"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": 579,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000717631.1",
"gene_hgnc_id": 50504,
"gene_symbol": "EP300-AS1",
"hgvs_c": "n.358-10603C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000717631.1",
"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": 346,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000717632.1",
"gene_hgnc_id": 50504,
"gene_symbol": "EP300-AS1",
"hgvs_c": "n.268-5948C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000717632.1",
"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": 302,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000774286.1",
"gene_hgnc_id": 50504,
"gene_symbol": "EP300-AS1",
"hgvs_c": "n.78-10603C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000774286.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.000743398004429277,
"dbsnp": "rs115849119",
"effect": "intron_variant",
"frequency_reference_population": 0.0014229759,
"gene_hgnc_id": 3373,
"gene_symbol": "EP300",
"gnomad_exomes_ac": 1120,
"gnomad_exomes_af": 0.000766433,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_ac": 1176,
"gnomad_genomes_af": 0.00772637,
"gnomad_genomes_homalt": 13,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 18,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Rubinstein-Taybi syndrome due to EP300 haploinsufficiency|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -1.375,
"pos": 41152194,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.035999998450279236,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001429.4"
}
]
}