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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: 19-42226405-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=42226405&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 42226405,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000301215.8",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF526",
"gene_hgnc_id": 29415,
"hgvs_c": "c.2002G>C",
"hgvs_p": "p.Ala668Pro",
"transcript": "NM_133444.3",
"protein_id": "NP_597701.1",
"transcript_support_level": null,
"aa_start": 668,
"aa_end": null,
"aa_length": 670,
"cds_start": 2002,
"cds_end": null,
"cds_length": 2013,
"cdna_start": 2186,
"cdna_end": null,
"cdna_length": 3982,
"mane_select": "ENST00000301215.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF526",
"gene_hgnc_id": 29415,
"hgvs_c": "c.2002G>C",
"hgvs_p": "p.Ala668Pro",
"transcript": "ENST00000301215.8",
"protein_id": "ENSP00000301215.2",
"transcript_support_level": 1,
"aa_start": 668,
"aa_end": null,
"aa_length": 670,
"cds_start": 2002,
"cds_end": null,
"cds_length": 2013,
"cdna_start": 2186,
"cdna_end": null,
"cdna_length": 3982,
"mane_select": "NM_133444.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288671",
"gene_hgnc_id": null,
"hgvs_c": "c.91+5652C>G",
"hgvs_p": null,
"transcript": "ENST00000678490.1",
"protein_id": "ENSP00000502878.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 69,
"cds_start": -4,
"cds_end": null,
"cds_length": 211,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF526",
"gene_hgnc_id": 29415,
"hgvs_c": "c.2002G>C",
"hgvs_p": "p.Ala668Pro",
"transcript": "NM_001314033.3",
"protein_id": "NP_001300962.1",
"transcript_support_level": null,
"aa_start": 668,
"aa_end": null,
"aa_length": 670,
"cds_start": 2002,
"cds_end": null,
"cds_length": 2013,
"cdna_start": 2434,
"cdna_end": null,
"cdna_length": 4230,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF526",
"gene_hgnc_id": 29415,
"hgvs_c": "c.2002G>C",
"hgvs_p": "p.Ala668Pro",
"transcript": "ENST00000710326.1",
"protein_id": "ENSP00000518206.1",
"transcript_support_level": null,
"aa_start": 668,
"aa_end": null,
"aa_length": 670,
"cds_start": 2002,
"cds_end": null,
"cds_length": 2013,
"cdna_start": 2206,
"cdna_end": null,
"cdna_length": 4002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSK3A",
"gene_hgnc_id": 4616,
"hgvs_c": "c.108C>G",
"hgvs_p": "p.Gly36Gly",
"transcript": "ENST00000677025.1",
"protein_id": "ENSP00000503204.1",
"transcript_support_level": null,
"aa_start": 36,
"aa_end": null,
"aa_length": 95,
"cds_start": 108,
"cds_end": null,
"cds_length": 288,
"cdna_start": 110,
"cdna_end": null,
"cdna_length": 290,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ZNF526",
"gene_hgnc_id": 29415,
"dbsnp": "rs758206052",
"frequency_reference_population": 0.000030357964,
"hom_count_reference_population": 2,
"allele_count_reference_population": 49,
"gnomad_exomes_af": 0.0000307826,
"gnomad_genomes_af": 0.0000262798,
"gnomad_exomes_ac": 45,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0912523865699768,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.05,
"revel_prediction": "Benign",
"alphamissense_score": 0.3177,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.667,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000301215.8",
"gene_symbol": "ZNF526",
"hgnc_id": 29415,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2002G>C",
"hgvs_p": "p.Ala668Pro"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000678490.1",
"gene_symbol": "ENSG00000288671",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.91+5652C>G",
"hgvs_p": null
},
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000677025.1",
"gene_symbol": "GSK3A",
"hgnc_id": 4616,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.108C>G",
"hgvs_p": "p.Gly36Gly"
}
],
"clinvar_disease": "Inborn genetic diseases,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not specified|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}