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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: 3-128638096-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=128638096&ref=G&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": "RPN1",
"hgnc_id": 10381,
"hgvs_c": "c.336C>A",
"hgvs_p": "p.Phe112Leu",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_002950.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 1,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.9056,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.39,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.132646381855011,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 607,
"aa_ref": "F",
"aa_start": 112,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2284,
"cdna_start": 354,
"cds_end": null,
"cds_length": 1824,
"cds_start": 336,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_002950.4",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "c.336C>A",
"hgvs_p": "p.Phe112Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000296255.8",
"protein_coding": true,
"protein_id": "NP_002941.1",
"strand": false,
"transcript": "NM_002950.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 607,
"aa_ref": "F",
"aa_start": 112,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2284,
"cdna_start": 354,
"cds_end": null,
"cds_length": 1824,
"cds_start": 336,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000296255.8",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "c.336C>A",
"hgvs_p": "p.Phe112Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002950.4",
"protein_coding": true,
"protein_id": "ENSP00000296255.3",
"strand": false,
"transcript": "ENST00000296255.8",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 621,
"aa_ref": "F",
"aa_start": 112,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2329,
"cdna_start": 358,
"cds_end": null,
"cds_length": 1866,
"cds_start": 336,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000874295.1",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "c.336C>A",
"hgvs_p": "p.Phe112Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544354.1",
"strand": false,
"transcript": "ENST00000874295.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 606,
"aa_ref": "F",
"aa_start": 112,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2329,
"cdna_start": 401,
"cds_end": null,
"cds_length": 1821,
"cds_start": 336,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000916581.1",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "c.336C>A",
"hgvs_p": "p.Phe112Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586640.1",
"strand": false,
"transcript": "ENST00000916581.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 604,
"aa_ref": "F",
"aa_start": 110,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2292,
"cdna_start": 369,
"cds_end": null,
"cds_length": 1815,
"cds_start": 330,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000916582.1",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "c.330C>A",
"hgvs_p": "p.Phe110Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586641.1",
"strand": false,
"transcript": "ENST00000916582.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 602,
"aa_ref": "F",
"aa_start": 112,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2081,
"cdna_start": 352,
"cds_end": null,
"cds_length": 1809,
"cds_start": 336,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000916584.1",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "c.336C>A",
"hgvs_p": "p.Phe112Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586643.1",
"strand": false,
"transcript": "ENST00000916584.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 596,
"aa_ref": "F",
"aa_start": 112,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2248,
"cdna_start": 356,
"cds_end": null,
"cds_length": 1791,
"cds_start": 336,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000916583.1",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "c.336C>A",
"hgvs_p": "p.Phe112Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586642.1",
"strand": false,
"transcript": "ENST00000916583.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 567,
"aa_ref": "F",
"aa_start": 112,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2177,
"cdna_start": 366,
"cds_end": null,
"cds_length": 1704,
"cds_start": 336,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000874294.1",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "c.336C>A",
"hgvs_p": "p.Phe112Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544353.1",
"strand": false,
"transcript": "ENST00000874294.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 537,
"aa_ref": "F",
"aa_start": 112,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2115,
"cdna_start": 395,
"cds_end": null,
"cds_length": 1614,
"cds_start": 336,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000874292.1",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "c.336C>A",
"hgvs_p": "p.Phe112Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544351.1",
"strand": false,
"transcript": "ENST00000874292.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 501,
"aa_ref": "F",
"aa_start": 112,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1958,
"cdna_start": 354,
"cds_end": null,
"cds_length": 1506,
"cds_start": 336,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000955675.1",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "c.336C>A",
"hgvs_p": "p.Phe112Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625734.1",
"strand": false,
"transcript": "ENST00000955675.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 423,
"aa_ref": "F",
"aa_start": 112,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1746,
"cdna_start": 368,
"cds_end": null,
"cds_length": 1272,
"cds_start": 336,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000874293.1",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "c.336C>A",
"hgvs_p": "p.Phe112Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544352.1",
"strand": false,
"transcript": "ENST00000874293.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 435,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2137,
"cdna_start": null,
"cds_end": null,
"cds_length": 1308,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000497289.5",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "c.-181C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000417529.1",
"strand": false,
"transcript": "ENST00000497289.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 483,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1911,
"cdna_start": null,
"cds_end": null,
"cds_length": 1452,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000874296.1",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "c.262-5939C>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544355.1",
"strand": false,
"transcript": "ENST00000874296.1",
"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": 526,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000476931.1",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "n.*82C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000419384.1",
"strand": false,
"transcript": "ENST00000476931.1",
"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": 558,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000479113.1",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "n.282C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000479113.1",
"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": 566,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000495462.5",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "n.232C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000495462.5",
"transcript_support_level": 3
},
{
"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": 526,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000476931.1",
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"hgvs_c": "n.*82C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000419384.1",
"strand": false,
"transcript": "ENST00000476931.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1191615052",
"effect": "missense_variant",
"frequency_reference_population": 6.8539157e-7,
"gene_hgnc_id": 10381,
"gene_symbol": "RPN1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.85392e-7,
"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": 1.326,
"pos": 128638096,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.047,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002950.4"
}
]
}