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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: 1-44801630-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=44801630&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 7,
"criteria": [
"PM2",
"BP4_Moderate",
"BP7",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "PLK3",
"hgnc_id": 2154,
"hgvs_c": "c.444C>T",
"hgvs_p": "p.Ala148Ala",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": -5,
"transcript": "NM_004073.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP7,BS2",
"acmg_score": -5,
"allele_count_reference_population": 5,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.36,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.36000001430511475,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 646,
"aa_ref": "A",
"aa_start": 148,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2340,
"cdna_start": 531,
"cds_end": null,
"cds_length": 1941,
"cds_start": 444,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_004073.4",
"gene_hgnc_id": 2154,
"gene_symbol": "PLK3",
"hgvs_c": "c.444C>T",
"hgvs_p": "p.Ala148Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000372201.5",
"protein_coding": true,
"protein_id": "NP_004064.2",
"strand": true,
"transcript": "NM_004073.4",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 646,
"aa_ref": "A",
"aa_start": 148,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2340,
"cdna_start": 531,
"cds_end": null,
"cds_length": 1941,
"cds_start": 444,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000372201.5",
"gene_hgnc_id": 2154,
"gene_symbol": "PLK3",
"hgvs_c": "c.444C>T",
"hgvs_p": "p.Ala148Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004073.4",
"protein_coding": true,
"protein_id": "ENSP00000361275.4",
"strand": true,
"transcript": "ENST00000372201.5",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 654,
"aa_ref": "A",
"aa_start": 148,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2395,
"cdna_start": 562,
"cds_end": null,
"cds_length": 1965,
"cds_start": 444,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000854219.1",
"gene_hgnc_id": 2154,
"gene_symbol": "PLK3",
"hgvs_c": "c.444C>T",
"hgvs_p": "p.Ala148Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000524278.1",
"strand": true,
"transcript": "ENST00000854219.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 646,
"aa_ref": "A",
"aa_start": 148,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2345,
"cdna_start": 531,
"cds_end": null,
"cds_length": 1941,
"cds_start": 444,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000850614.1",
"gene_hgnc_id": 2154,
"gene_symbol": "PLK3",
"hgvs_c": "c.444C>T",
"hgvs_p": "p.Ala148Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000520901.1",
"strand": true,
"transcript": "ENST00000850614.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 643,
"aa_ref": "A",
"aa_start": 148,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2317,
"cdna_start": 519,
"cds_end": null,
"cds_length": 1932,
"cds_start": 444,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000942821.1",
"gene_hgnc_id": 2154,
"gene_symbol": "PLK3",
"hgvs_c": "c.444C>T",
"hgvs_p": "p.Ala148Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612880.1",
"strand": true,
"transcript": "ENST00000942821.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 607,
"aa_ref": "A",
"aa_start": 109,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2179,
"cdna_start": 372,
"cds_end": null,
"cds_length": 1824,
"cds_start": 327,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000854220.1",
"gene_hgnc_id": 2154,
"gene_symbol": "PLK3",
"hgvs_c": "c.327C>T",
"hgvs_p": "p.Ala109Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000524279.1",
"strand": true,
"transcript": "ENST00000854220.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 511,
"aa_ref": "A",
"aa_start": 148,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1706,
"cdna_start": 531,
"cds_end": null,
"cds_length": 1536,
"cds_start": 444,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047444455.1",
"gene_hgnc_id": 2154,
"gene_symbol": "PLK3",
"hgvs_c": "c.444C>T",
"hgvs_p": "p.Ala148Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047300411.1",
"strand": true,
"transcript": "XM_047444455.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 330,
"aa_ref": "A",
"aa_start": 148,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1220,
"cdna_start": 531,
"cds_end": null,
"cds_length": 993,
"cds_start": 444,
"consequences": [
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047444463.1",
"gene_hgnc_id": 2154,
"gene_symbol": "PLK3",
"hgvs_c": "c.444C>T",
"hgvs_p": "p.Ala148Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047300419.1",
"strand": true,
"transcript": "XM_047444463.1",
"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": 2477,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000465443.5",
"gene_hgnc_id": 2154,
"gene_symbol": "PLK3",
"hgvs_c": "n.520C>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": "ENST00000465443.5",
"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": 761,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000476731.1",
"gene_hgnc_id": 2154,
"gene_symbol": "PLK3",
"hgvs_c": "n.-4C>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": "ENST00000476731.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs140199593",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0000034213488,
"gene_hgnc_id": 2154,
"gene_symbol": "PLK3",
"gnomad_exomes_ac": 5,
"gnomad_exomes_af": 0.00000342135,
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.096,
"pos": 44801630,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.10999999940395355,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.11,
"transcript": "NM_004073.4"
}
]
}