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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: 6-36323317-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=36323317&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "BNIP5",
"hgnc_id": 33769,
"hgvs_c": "c.1447C>T",
"hgvs_p": "p.Arg483Trp",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_001010903.5",
"verdict": "Likely_benign"
},
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000297259",
"hgnc_id": null,
"hgvs_c": "n.303+1030G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -2,
"transcript": "ENST00000746644.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 20,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1054,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.36,
"chr": "6",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Prostate cancer",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.09903928637504578,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 652,
"aa_ref": "R",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3735,
"cdna_start": 1628,
"cds_end": null,
"cds_length": 1959,
"cds_start": 1447,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001010903.5",
"gene_hgnc_id": 33769,
"gene_symbol": "BNIP5",
"hgvs_c": "c.1447C>T",
"hgvs_p": "p.Arg483Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000437635.3",
"protein_coding": true,
"protein_id": "NP_001010903.3",
"strand": false,
"transcript": "NM_001010903.5",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 652,
"aa_ref": "R",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3735,
"cdna_start": 1628,
"cds_end": null,
"cds_length": 1959,
"cds_start": 1447,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000437635.3",
"gene_hgnc_id": 33769,
"gene_symbol": "BNIP5",
"hgvs_c": "c.1447C>T",
"hgvs_p": "p.Arg483Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001010903.5",
"protein_coding": true,
"protein_id": "ENSP00000418983.1",
"strand": false,
"transcript": "ENST00000437635.3",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 651,
"aa_ref": "R",
"aa_start": 482,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3858,
"cdna_start": 1747,
"cds_end": null,
"cds_length": 1956,
"cds_start": 1444,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000860604.1",
"gene_hgnc_id": 33769,
"gene_symbol": "BNIP5",
"hgvs_c": "c.1444C>T",
"hgvs_p": "p.Arg482Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530663.1",
"strand": false,
"transcript": "ENST00000860604.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 625,
"aa_ref": "R",
"aa_start": 456,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2154,
"cdna_start": 1544,
"cds_end": null,
"cds_length": 1878,
"cds_start": 1366,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000860607.1",
"gene_hgnc_id": 33769,
"gene_symbol": "BNIP5",
"hgvs_c": "c.1366C>T",
"hgvs_p": "p.Arg456Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530666.1",
"strand": false,
"transcript": "ENST00000860607.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 608,
"aa_ref": "R",
"aa_start": 439,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2106,
"cdna_start": 1496,
"cds_end": null,
"cds_length": 1827,
"cds_start": 1315,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000860606.1",
"gene_hgnc_id": 33769,
"gene_symbol": "BNIP5",
"hgvs_c": "c.1315C>T",
"hgvs_p": "p.Arg439Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530665.1",
"strand": false,
"transcript": "ENST00000860606.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 608,
"aa_ref": "R",
"aa_start": 439,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3601,
"cdna_start": 1494,
"cds_end": null,
"cds_length": 1827,
"cds_start": 1315,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000944763.1",
"gene_hgnc_id": 33769,
"gene_symbol": "BNIP5",
"hgvs_c": "c.1315C>T",
"hgvs_p": "p.Arg439Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000614822.1",
"strand": false,
"transcript": "ENST00000944763.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 567,
"aa_ref": "R",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1983,
"cdna_start": 1628,
"cds_end": null,
"cds_length": 1704,
"cds_start": 1447,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000860605.1",
"gene_hgnc_id": 33769,
"gene_symbol": "BNIP5",
"hgvs_c": "c.1447C>T",
"hgvs_p": "p.Arg483Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530664.1",
"strand": false,
"transcript": "ENST00000860605.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 652,
"aa_ref": "R",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4584,
"cdna_start": 2477,
"cds_end": null,
"cds_length": 1959,
"cds_start": 1447,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_011514596.3",
"gene_hgnc_id": 33769,
"gene_symbol": "BNIP5",
"hgvs_c": "c.1447C>T",
"hgvs_p": "p.Arg483Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512898.1",
"strand": false,
"transcript": "XM_011514596.3",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 651,
"aa_ref": "R",
"aa_start": 482,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3732,
"cdna_start": 1625,
"cds_end": null,
"cds_length": 1956,
"cds_start": 1444,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_011514597.3",
"gene_hgnc_id": 33769,
"gene_symbol": "BNIP5",
"hgvs_c": "c.1444C>T",
"hgvs_p": "p.Arg482Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512899.1",
"strand": false,
"transcript": "XM_011514597.3",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 404,
"aa_ref": "R",
"aa_start": 235,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3121,
"cdna_start": 1014,
"cds_end": null,
"cds_length": 1215,
"cds_start": 703,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011514598.3",
"gene_hgnc_id": 33769,
"gene_symbol": "BNIP5",
"hgvs_c": "c.703C>T",
"hgvs_p": "p.Arg235Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512900.1",
"strand": false,
"transcript": "XM_011514598.3",
"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": 671,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000746644.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000297259",
"hgvs_c": "n.303+1030G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000746644.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs193920980",
"effect": "missense_variant",
"frequency_reference_population": 0.000012390683,
"gene_hgnc_id": 33769,
"gene_symbol": "BNIP5",
"gnomad_exomes_ac": 12,
"gnomad_exomes_af": 0.00000820872,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 8,
"gnomad_genomes_af": 0.0000525431,
"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": "Uncertain significance",
"phenotype_combined": "Prostate cancer",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.656,
"pos": 36323317,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.093,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_001010903.5"
}
]
}