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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: 15-40212490-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=40212490&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "BUB1B",
"hgnc_id": 1149,
"hgvs_c": "c.2386-9G>A",
"hgvs_p": null,
"inheritance_mode": "AR,AD",
"pathogenic_score": 2,
"score": -4,
"transcript": "NM_001211.6",
"verdict": "Likely_benign"
},
{
"benign_score": 6,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC107984763",
"hgnc_id": null,
"hgvs_c": "n.217+26995C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -4,
"transcript": "XR_001751506.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate",
"acmg_score": -4,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.73,
"chr": "15",
"clinvar_classification": "Likely benign",
"clinvar_disease": "Mosaic variegated aneuploidy syndrome 1",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7300000190734863,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1050,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3669,
"cdna_start": null,
"cds_end": null,
"cds_length": 3153,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 23,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001211.6",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.2386-9G>A",
"hgvs_p": null,
"intron_rank": 18,
"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": null,
"aa_end": null,
"aa_length": 1050,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3669,
"cdna_start": null,
"cds_end": null,
"cds_length": 3153,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 23,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000287598.11",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.2386-9G>A",
"hgvs_p": null,
"intron_rank": 18,
"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": null,
"aa_end": null,
"aa_length": 1064,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3628,
"cdna_start": null,
"cds_end": null,
"cds_length": 3195,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 23,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000412359.7",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.2428-9G>A",
"hgvs_p": null,
"intron_rank": 18,
"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": null,
"aa_end": null,
"aa_length": 1084,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3781,
"cdna_start": null,
"cds_end": null,
"cds_length": 3255,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000918306.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.2488-9G>A",
"hgvs_p": null,
"intron_rank": 19,
"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": null,
"aa_end": null,
"aa_length": 1056,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3683,
"cdna_start": null,
"cds_end": null,
"cds_length": 3171,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 23,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000918309.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.2404-9G>A",
"hgvs_p": null,
"intron_rank": 18,
"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": null,
"aa_end": null,
"aa_length": 1055,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3740,
"cdna_start": null,
"cds_end": null,
"cds_length": 3168,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 23,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000897791.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.2401-9G>A",
"hgvs_p": null,
"intron_rank": 18,
"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": null,
"aa_end": null,
"aa_length": 1035,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3667,
"cdna_start": null,
"cds_end": null,
"cds_length": 3108,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 23,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000897792.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.2341-9G>A",
"hgvs_p": null,
"intron_rank": 18,
"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": null,
"aa_end": null,
"aa_length": 1030,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3652,
"cdna_start": null,
"cds_end": null,
"cds_length": 3093,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000918305.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.2326-9G>A",
"hgvs_p": null,
"intron_rank": 17,
"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": null,
"aa_end": null,
"aa_length": 916,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3244,
"cdna_start": null,
"cds_end": null,
"cds_length": 2751,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 20,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000918310.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1984-9G>A",
"hgvs_p": null,
"intron_rank": 15,
"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": null,
"aa_end": null,
"aa_length": 891,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3189,
"cdna_start": null,
"cds_end": null,
"cds_length": 2676,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 20,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000918308.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1909-9G>A",
"hgvs_p": null,
"intron_rank": 15,
"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": null,
"aa_end": null,
"aa_length": 868,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3133,
"cdna_start": null,
"cds_end": null,
"cds_length": 2607,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000918307.1",
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"hgvs_c": "c.1840-9G>A",
"hgvs_p": null,
"intron_rank": 14,
"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": "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.217+26995C>T",
"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": "Benign",
"dbscsnv_ada_score": 0.0013334204799532,
"dbsnp": "rs1189315798",
"effect": "intron_variant",
"frequency_reference_population": 0.0000012433002,
"gene_hgnc_id": 1149,
"gene_symbol": "BUB1B",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.86596e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657194,
"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": "Likely benign",
"phenotype_combined": "Mosaic variegated aneuploidy syndrome 1",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.772,
"pos": 40212490,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.017999999225139618,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.03,
"transcript": "NM_001211.6"
}
]
}