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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: 19-12349856-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=12349856&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ZNF442",
"hgnc_id": 20877,
"hgvs_c": "c.1729T>C",
"hgvs_p": "p.Cys577Arg",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_030824.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": 0.6098,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.12,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.6738091707229614,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 627,
"aa_ref": "C",
"aa_start": 577,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6274,
"cdna_start": 2362,
"cds_end": null,
"cds_length": 1884,
"cds_start": 1729,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_030824.3",
"gene_hgnc_id": 20877,
"gene_symbol": "ZNF442",
"hgvs_c": "c.1729T>C",
"hgvs_p": "p.Cys577Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000242804.9",
"protein_coding": true,
"protein_id": "NP_110451.1",
"strand": false,
"transcript": "NM_030824.3",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 627,
"aa_ref": "C",
"aa_start": 577,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6274,
"cdna_start": 2362,
"cds_end": null,
"cds_length": 1884,
"cds_start": 1729,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000242804.9",
"gene_hgnc_id": 20877,
"gene_symbol": "ZNF442",
"hgvs_c": "c.1729T>C",
"hgvs_p": "p.Cys577Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_030824.3",
"protein_coding": true,
"protein_id": "ENSP00000242804.4",
"strand": false,
"transcript": "ENST00000242804.9",
"transcript_support_level": 2
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 627,
"aa_ref": "C",
"aa_start": 577,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1884,
"cdna_start": 1729,
"cds_end": null,
"cds_length": 1884,
"cds_start": 1729,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000545749.2",
"gene_hgnc_id": 20877,
"gene_symbol": "ZNF442",
"hgvs_c": "c.1729T>C",
"hgvs_p": "p.Cys577Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000440162.2",
"strand": false,
"transcript": "ENST00000545749.2",
"transcript_support_level": 5
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 558,
"aa_ref": "C",
"aa_start": 508,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5587,
"cdna_start": 1675,
"cds_end": null,
"cds_length": 1677,
"cds_start": 1522,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001363774.2",
"gene_hgnc_id": 20877,
"gene_symbol": "ZNF442",
"hgvs_c": "c.1522T>C",
"hgvs_p": "p.Cys508Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001350703.1",
"strand": false,
"transcript": "NM_001363774.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 558,
"aa_ref": "C",
"aa_start": 508,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1906,
"cdna_start": 1633,
"cds_end": null,
"cds_length": 1677,
"cds_start": 1522,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000438182.5",
"gene_hgnc_id": 20877,
"gene_symbol": "ZNF442",
"hgvs_c": "c.1522T>C",
"hgvs_p": "p.Cys508Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000388634.1",
"strand": false,
"transcript": "ENST00000438182.5",
"transcript_support_level": 2
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 620,
"aa_ref": "C",
"aa_start": 570,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5764,
"cdna_start": 1852,
"cds_end": null,
"cds_length": 1863,
"cds_start": 1708,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_006722908.4",
"gene_hgnc_id": 20877,
"gene_symbol": "ZNF442",
"hgvs_c": "c.1708T>C",
"hgvs_p": "p.Cys570Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006722971.1",
"strand": false,
"transcript": "XM_006722908.4",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 570,
"aa_ref": "C",
"aa_start": 520,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5581,
"cdna_start": 1669,
"cds_end": null,
"cds_length": 1713,
"cds_start": 1558,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017027316.2",
"gene_hgnc_id": 20877,
"gene_symbol": "ZNF442",
"hgvs_c": "c.1558T>C",
"hgvs_p": "p.Cys520Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882805.2",
"strand": false,
"transcript": "XM_017027316.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 570,
"aa_ref": "C",
"aa_start": 520,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5842,
"cdna_start": 1930,
"cds_end": null,
"cds_length": 1713,
"cds_start": 1558,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_017027317.2",
"gene_hgnc_id": 20877,
"gene_symbol": "ZNF442",
"hgvs_c": "c.1558T>C",
"hgvs_p": "p.Cys520Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882806.1",
"strand": false,
"transcript": "XM_017027317.2",
"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": 3407,
"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": "XR_007067014.1",
"gene_hgnc_id": 20877,
"gene_symbol": "ZNF442",
"hgvs_c": "n.1651T>C",
"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": "XR_007067014.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": 0.0000013681313,
"gene_hgnc_id": 20877,
"gene_symbol": "ZNF442",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000136813,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.222,
"pos": 12349856,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.164,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_030824.3"
}
]
}