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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: 19-33301626-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=33301626&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 17,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "CEBPA",
"hgnc_id": 1833,
"hgvs_c": "c.894C>T",
"hgvs_p": "p.Leu298Leu",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -17,
"transcript": "NM_001287424.2",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000267727",
"hgnc_id": null,
"hgvs_c": "n.348G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000587312.1",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "CEBPA-DT",
"hgnc_id": 25710,
"hgvs_c": "n.-128G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000718467.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_score": -17,
"allele_count_reference_population": 83,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.58,
"chr": "19",
"clinvar_classification": "Likely benign",
"clinvar_disease": "Acute myeloid leukemia,CEBPA-related disorder,Inborn genetic diseases,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.5799999833106995,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 358,
"aa_ref": "L",
"aa_start": 263,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2601,
"cdna_start": 909,
"cds_end": null,
"cds_length": 1077,
"cds_start": 789,
"consequences": [
"synonymous_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_004364.5",
"gene_hgnc_id": 1833,
"gene_symbol": "CEBPA",
"hgvs_c": "c.789C>T",
"hgvs_p": "p.Leu263Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000498907.3",
"protein_coding": true,
"protein_id": "NP_004355.2",
"strand": false,
"transcript": "NM_004364.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 358,
"aa_ref": "L",
"aa_start": 263,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2601,
"cdna_start": 909,
"cds_end": null,
"cds_length": 1077,
"cds_start": 789,
"consequences": [
"synonymous_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000498907.3",
"gene_hgnc_id": 1833,
"gene_symbol": "CEBPA",
"hgvs_c": "c.789C>T",
"hgvs_p": "p.Leu263Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004364.5",
"protein_coding": true,
"protein_id": "ENSP00000427514.1",
"strand": false,
"transcript": "ENST00000498907.3",
"transcript_support_level": 6
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 393,
"aa_ref": "L",
"aa_start": 298,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2601,
"cdna_start": 909,
"cds_end": null,
"cds_length": 1182,
"cds_start": 894,
"consequences": [
"synonymous_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001287424.2",
"gene_hgnc_id": 1833,
"gene_symbol": "CEBPA",
"hgvs_c": "c.894C>T",
"hgvs_p": "p.Leu298Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001274353.1",
"strand": false,
"transcript": "NM_001287424.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 344,
"aa_ref": "L",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2601,
"cdna_start": 909,
"cds_end": null,
"cds_length": 1035,
"cds_start": 747,
"consequences": [
"synonymous_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001287435.2",
"gene_hgnc_id": 1833,
"gene_symbol": "CEBPA",
"hgvs_c": "c.747C>T",
"hgvs_p": "p.Leu249Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001274364.1",
"strand": false,
"transcript": "NM_001287435.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 239,
"aa_ref": "L",
"aa_start": 144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2601,
"cdna_start": 909,
"cds_end": null,
"cds_length": 720,
"cds_start": 432,
"consequences": [
"synonymous_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001285829.2",
"gene_hgnc_id": 1833,
"gene_symbol": "CEBPA",
"hgvs_c": "c.432C>T",
"hgvs_p": "p.Leu144Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001272758.1",
"strand": false,
"transcript": "NM_001285829.2",
"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": 482,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000587312.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000267727",
"hgvs_c": "n.348G>A",
"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": "ENST00000587312.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 722,
"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": "ENST00000718467.1",
"gene_hgnc_id": 25710,
"gene_symbol": "CEBPA-DT",
"hgvs_c": "n.-128G>A",
"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": "ENST00000718467.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs552131738",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000052447995,
"gene_hgnc_id": 1833,
"gene_symbol": "CEBPA",
"gnomad_exomes_ac": 42,
"gnomad_exomes_af": 0.0000293439,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 41,
"gnomad_genomes_af": 0.000271135,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "Acute myeloid leukemia|not specified|CEBPA-related disorder|Inborn genetic diseases",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.891,
"pos": 33301626,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001287424.2"
}
]
}