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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: 17-28364287-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=28364287&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SEBOX",
"hgnc_id": 32942,
"hgvs_c": "c.554T>A",
"hgvs_p": "p.Val185Asp",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_001080837.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000258924",
"hgnc_id": null,
"hgvs_c": "n.555+3440A>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000591482.1",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"downstream_gene_variant"
],
"gene_symbol": "ENSG00000273171",
"hgnc_id": null,
"hgvs_c": "c.*405T>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000555059.2",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "SARM1",
"hgnc_id": 17074,
"hgvs_c": "n.-69A>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000379061.8",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 3,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1597,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.43,
"chr": "17",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.1391741931438446,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 190,
"aa_ref": "V",
"aa_start": 185,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1383,
"cdna_start": 602,
"cds_end": null,
"cds_length": 573,
"cds_start": 554,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001080837.4",
"gene_hgnc_id": 32942,
"gene_symbol": "SEBOX",
"hgvs_c": "c.554T>A",
"hgvs_p": "p.Val185Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000536498.6",
"protein_coding": true,
"protein_id": "NP_001074306.3",
"strand": false,
"transcript": "NM_001080837.4",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 190,
"aa_ref": "V",
"aa_start": 185,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1383,
"cdna_start": 602,
"cds_end": null,
"cds_length": 573,
"cds_start": 554,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000536498.6",
"gene_hgnc_id": 32942,
"gene_symbol": "SEBOX",
"hgvs_c": "c.554T>A",
"hgvs_p": "p.Val185Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001080837.4",
"protein_coding": true,
"protein_id": "ENSP00000444503.3",
"strand": false,
"transcript": "ENST00000536498.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1050,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000591482.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258924",
"hgvs_c": "n.555+3440A>T",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000591482.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 148,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 851,
"cdna_start": null,
"cds_end": null,
"cds_length": 447,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000555059.2",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000273171",
"hgvs_c": "c.*405T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000452347.3",
"strand": true,
"transcript": "ENST00000555059.2",
"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": 1921,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000379061.8",
"gene_hgnc_id": 17074,
"gene_symbol": "SARM1",
"hgvs_c": "n.-69A>T",
"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": "ENST00000379061.8",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs782522260",
"effect": "missense_variant",
"frequency_reference_population": 0.0000020610512,
"gene_hgnc_id": 32942,
"gene_symbol": "SEBOX",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.00000206105,
"gnomad_exomes_homalt": 0,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.18,
"pos": 28364287,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.279,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001080837.4"
}
]
}