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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: 15-40206195-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=40206195&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 9,
"criteria": [
"BP4_Strong",
"BP6",
"BS1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "BUB1B",
"hgnc_id": 1149,
"hgvs_c": "c.1746A>C",
"hgvs_p": "p.Thr582Thr",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -9,
"transcript": "NM_001211.6",
"verdict": "Benign"
},
{
"benign_score": 5,
"criteria": [
"BP4_Strong",
"BP6"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC107984763",
"hgnc_id": null,
"hgvs_c": "n.218-25994T>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -5,
"transcript": "XR_001751506.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1",
"acmg_score": -9,
"allele_count_reference_population": 73,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.93,
"chr": "15",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Inborn genetic diseases,Mosaic variegated aneuploidy syndrome 1,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.9300000071525574,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1050,
"aa_ref": "T",
"aa_start": 582,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3669,
"cdna_start": 1898,
"cds_end": null,
"cds_length": 3153,
"cds_start": 1746,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_001211.6",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1746A>C",
"hgvs_p": "p.Thr582Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000287598.11",
"protein_coding": true,
"protein_id": "NP_001202.5",
"strand": true,
"transcript": "NM_001211.6",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1050,
"aa_ref": "T",
"aa_start": 582,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3669,
"cdna_start": 1898,
"cds_end": null,
"cds_length": 3153,
"cds_start": 1746,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000287598.11",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1746A>C",
"hgvs_p": "p.Thr582Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001211.6",
"protein_coding": true,
"protein_id": "ENSP00000287598.7",
"strand": true,
"transcript": "ENST00000287598.11",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1064,
"aa_ref": "T",
"aa_start": 596,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3628,
"cdna_start": 1942,
"cds_end": null,
"cds_length": 3195,
"cds_start": 1788,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000412359.7",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1788A>C",
"hgvs_p": "p.Thr596Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000398470.3",
"strand": true,
"transcript": "ENST00000412359.7",
"transcript_support_level": 2
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1084,
"aa_ref": "T",
"aa_start": 616,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3781,
"cdna_start": 2010,
"cds_end": null,
"cds_length": 3255,
"cds_start": 1848,
"consequences": [
"synonymous_variant"
],
"exon_count": 24,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000918306.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1848A>C",
"hgvs_p": "p.Thr616Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000588365.1",
"strand": true,
"transcript": "ENST00000918306.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1056,
"aa_ref": "T",
"aa_start": 588,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3683,
"cdna_start": 1912,
"cds_end": null,
"cds_length": 3171,
"cds_start": 1764,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000918309.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1764A>C",
"hgvs_p": "p.Thr588Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000588368.1",
"strand": true,
"transcript": "ENST00000918309.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1055,
"aa_ref": "T",
"aa_start": 587,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3740,
"cdna_start": 1956,
"cds_end": null,
"cds_length": 3168,
"cds_start": 1761,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000897791.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1761A>C",
"hgvs_p": "p.Thr587Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000567850.1",
"strand": true,
"transcript": "ENST00000897791.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1035,
"aa_ref": "T",
"aa_start": 567,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3667,
"cdna_start": 1899,
"cds_end": null,
"cds_length": 3108,
"cds_start": 1701,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000897792.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1701A>C",
"hgvs_p": "p.Thr567Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000567851.1",
"strand": true,
"transcript": "ENST00000897792.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1030,
"aa_ref": "T",
"aa_start": 562,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3652,
"cdna_start": 1881,
"cds_end": null,
"cds_length": 3093,
"cds_start": 1686,
"consequences": [
"synonymous_variant"
],
"exon_count": 22,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000918305.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1686A>C",
"hgvs_p": "p.Thr562Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000588364.1",
"strand": true,
"transcript": "ENST00000918305.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 916,
"aa_ref": "T",
"aa_start": 448,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3244,
"cdna_start": 1478,
"cds_end": null,
"cds_length": 2751,
"cds_start": 1344,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000918310.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1344A>C",
"hgvs_p": "p.Thr448Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000588369.1",
"strand": true,
"transcript": "ENST00000918310.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 891,
"aa_ref": "T",
"aa_start": 423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3189,
"cdna_start": 1418,
"cds_end": null,
"cds_length": 2676,
"cds_start": 1269,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000918308.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1269A>C",
"hgvs_p": "p.Thr423Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000588367.1",
"strand": true,
"transcript": "ENST00000918308.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 868,
"aa_ref": "T",
"aa_start": 400,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3133,
"cdna_start": 1362,
"cds_end": null,
"cds_length": 2607,
"cds_start": 1200,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000918307.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1200A>C",
"hgvs_p": "p.Thr400Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000588366.1",
"strand": true,
"transcript": "ENST00000918307.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 630,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000558972.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "n.551A>C",
"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": "ENST00000558972.1",
"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": 2984,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_001751506.2",
"gene_hgnc_id": null,
"gene_symbol": "LOC107984763",
"hgvs_c": "n.218-25994T>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_001751506.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs373105304",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000045227003,
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"gnomad_exomes_ac": 37,
"gnomad_exomes_af": 0.0000253108,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 36,
"gnomad_genomes_af": 0.000236447,
"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": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Mosaic variegated aneuploidy syndrome 1|not provided|Inborn genetic diseases",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.412,
"pos": 40206195,
"ref": "A",
"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_001211.6"
}
]
}