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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: 2-132645512-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=132645512&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 8,
"criteria": [
"BP4_Strong",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GPR39",
"hgnc_id": 4496,
"hgvs_c": "c.1268C>G",
"hgvs_p": "p.Ser423Cys",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -8,
"transcript": "NM_001508.3",
"verdict": "Benign"
},
{
"benign_score": 8,
"criteria": [
"BP4_Strong",
"BS2"
],
"effects": [
"3_prime_UTR_variant"
],
"gene_symbol": "LYPD1",
"hgnc_id": 28431,
"hgvs_c": "c.*533G>C",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -8,
"transcript": "NM_001321234.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_score": -8,
"allele_count_reference_population": 3687,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0816,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.54,
"chr": "2",
"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": 0.008588045835494995,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 453,
"aa_ref": "S",
"aa_start": 423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2576,
"cdna_start": 1506,
"cds_end": null,
"cds_length": 1362,
"cds_start": 1268,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001508.3",
"gene_hgnc_id": 4496,
"gene_symbol": "GPR39",
"hgvs_c": "c.1268C>G",
"hgvs_p": "p.Ser423Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000329321.4",
"protein_coding": true,
"protein_id": "NP_001499.1",
"strand": true,
"transcript": "NM_001508.3",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 453,
"aa_ref": "S",
"aa_start": 423,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2576,
"cdna_start": 1506,
"cds_end": null,
"cds_length": 1362,
"cds_start": 1268,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000329321.4",
"gene_hgnc_id": 4496,
"gene_symbol": "GPR39",
"hgvs_c": "c.1268C>G",
"hgvs_p": "p.Ser423Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001508.3",
"protein_coding": true,
"protein_id": "ENSP00000327417.3",
"strand": true,
"transcript": "ENST00000329321.4",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 141,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3458,
"cdna_start": null,
"cds_end": null,
"cds_length": 426,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_144586.7",
"gene_hgnc_id": 28431,
"gene_symbol": "LYPD1",
"hgvs_c": "c.*533G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000397463.3",
"protein_coding": true,
"protein_id": "NP_653187.3",
"strand": false,
"transcript": "NM_144586.7",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 141,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3458,
"cdna_start": null,
"cds_end": null,
"cds_length": 426,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000397463.3",
"gene_hgnc_id": 28431,
"gene_symbol": "LYPD1",
"hgvs_c": "c.*533G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_144586.7",
"protein_coding": true,
"protein_id": "ENSP00000380605.2",
"strand": false,
"transcript": "ENST00000397463.3",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 157,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3331,
"cdna_start": null,
"cds_end": null,
"cds_length": 474,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001321234.2",
"gene_hgnc_id": 28431,
"gene_symbol": "LYPD1",
"hgvs_c": "c.*533G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001308163.1",
"strand": false,
"transcript": "NM_001321234.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 95,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1803,
"cdna_start": null,
"cds_end": null,
"cds_length": 288,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000892683.1",
"gene_hgnc_id": 28431,
"gene_symbol": "LYPD1",
"hgvs_c": "c.*533G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000562742.1",
"strand": false,
"transcript": "ENST00000892683.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 89,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3481,
"cdna_start": null,
"cds_end": null,
"cds_length": 270,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001077427.4",
"gene_hgnc_id": 28431,
"gene_symbol": "LYPD1",
"hgvs_c": "c.*533G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001070895.1",
"strand": false,
"transcript": "NM_001077427.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 89,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3492,
"cdna_start": null,
"cds_end": null,
"cds_length": 270,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001321235.2",
"gene_hgnc_id": 28431,
"gene_symbol": "LYPD1",
"hgvs_c": "c.*533G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001308164.1",
"strand": false,
"transcript": "NM_001321235.2",
"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": 2013,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000470071.1",
"gene_hgnc_id": 4496,
"gene_symbol": "GPR39",
"hgvs_c": "n.971C>G",
"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": "ENST00000470071.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs61757692",
"effect": "missense_variant",
"frequency_reference_population": 0.0022858651,
"gene_hgnc_id": 4496,
"gene_symbol": "GPR39",
"gnomad_exomes_ac": 3431,
"gnomad_exomes_af": 0.00234852,
"gnomad_exomes_homalt": 9,
"gnomad_genomes_ac": 256,
"gnomad_genomes_af": 0.00168381,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 9,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.748,
"pos": 132645512,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.067,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001508.3"
}
]
}