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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: 15-64864975-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=64864975&ref=C&alt=A&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": "PLEKHO2",
"hgnc_id": 30026,
"hgvs_c": "c.560C>A",
"hgvs_p": "p.Pro187His",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_025201.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000249240",
"hgnc_id": null,
"hgvs_c": "c.483+3400C>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000437723.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.1273,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.42,
"chr": "15",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.2096259593963623,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 490,
"aa_ref": "P",
"aa_start": 187,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3689,
"cdna_start": 662,
"cds_end": null,
"cds_length": 1473,
"cds_start": 560,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_025201.5",
"gene_hgnc_id": 30026,
"gene_symbol": "PLEKHO2",
"hgvs_c": "c.560C>A",
"hgvs_p": "p.Pro187His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000323544.5",
"protein_coding": true,
"protein_id": "NP_079477.2",
"strand": true,
"transcript": "NM_025201.5",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 490,
"aa_ref": "P",
"aa_start": 187,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3689,
"cdna_start": 662,
"cds_end": null,
"cds_length": 1473,
"cds_start": 560,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000323544.5",
"gene_hgnc_id": 30026,
"gene_symbol": "PLEKHO2",
"hgvs_c": "c.560C>A",
"hgvs_p": "p.Pro187His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_025201.5",
"protein_coding": true,
"protein_id": "ENSP00000326706.4",
"strand": true,
"transcript": "ENST00000323544.5",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 440,
"aa_ref": "P",
"aa_start": 137,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3569,
"cdna_start": 544,
"cds_end": null,
"cds_length": 1323,
"cds_start": 410,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000616065.4",
"gene_hgnc_id": 30026,
"gene_symbol": "PLEKHO2",
"hgvs_c": "c.410C>A",
"hgvs_p": "p.Pro137His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000483505.1",
"strand": true,
"transcript": "ENST00000616065.4",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 226,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 750,
"cdna_start": null,
"cds_end": null,
"cds_length": 681,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000437723.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000249240",
"hgvs_c": "c.483+3400C>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000397942.1",
"strand": true,
"transcript": "ENST00000437723.1",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 488,
"aa_ref": "P",
"aa_start": 185,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6364,
"cdna_start": 3340,
"cds_end": null,
"cds_length": 1467,
"cds_start": 554,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000925882.1",
"gene_hgnc_id": 30026,
"gene_symbol": "PLEKHO2",
"hgvs_c": "c.554C>A",
"hgvs_p": "p.Pro185His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595941.1",
"strand": true,
"transcript": "ENST00000925882.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 457,
"aa_ref": "P",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3575,
"cdna_start": 548,
"cds_end": null,
"cds_length": 1374,
"cds_start": 461,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000925885.1",
"gene_hgnc_id": 30026,
"gene_symbol": "PLEKHO2",
"hgvs_c": "c.461C>A",
"hgvs_p": "p.Pro154His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595944.1",
"strand": true,
"transcript": "ENST00000925885.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 455,
"aa_ref": "P",
"aa_start": 152,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3582,
"cdna_start": 555,
"cds_end": null,
"cds_length": 1368,
"cds_start": 455,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000925883.1",
"gene_hgnc_id": 30026,
"gene_symbol": "PLEKHO2",
"hgvs_c": "c.455C>A",
"hgvs_p": "p.Pro152His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595942.1",
"strand": true,
"transcript": "ENST00000925883.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 440,
"aa_ref": "P",
"aa_start": 137,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3539,
"cdna_start": 512,
"cds_end": null,
"cds_length": 1323,
"cds_start": 410,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001195059.2",
"gene_hgnc_id": 30026,
"gene_symbol": "PLEKHO2",
"hgvs_c": "c.410C>A",
"hgvs_p": "p.Pro137His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001181988.1",
"strand": true,
"transcript": "NM_001195059.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 422,
"aa_ref": "P",
"aa_start": 119,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3485,
"cdna_start": 458,
"cds_end": null,
"cds_length": 1269,
"cds_start": 356,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000866141.1",
"gene_hgnc_id": 30026,
"gene_symbol": "PLEKHO2",
"hgvs_c": "c.356C>A",
"hgvs_p": "p.Pro119His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000536200.1",
"strand": true,
"transcript": "ENST00000866141.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 405,
"aa_ref": "P",
"aa_start": 102,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3432,
"cdna_start": 405,
"cds_end": null,
"cds_length": 1218,
"cds_start": 305,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000925884.1",
"gene_hgnc_id": 30026,
"gene_symbol": "PLEKHO2",
"hgvs_c": "c.305C>A",
"hgvs_p": "p.Pro102His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595943.1",
"strand": true,
"transcript": "ENST00000925884.1",
"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": 1178,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000502574.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000249240",
"hgvs_c": "n.617+3400C>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000502574.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 30026,
"gene_symbol": "PLEKHO2",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.54,
"pos": 64864975,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.121,
"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_025201.5"
}
]
}