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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: 8-144055135-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=144055135&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 144055135,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000618853.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPLAH",
"gene_hgnc_id": 8149,
"hgvs_c": "c.2303G>A",
"hgvs_p": "p.Arg768His",
"transcript": "NM_017570.5",
"protein_id": "NP_060040.1",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 1288,
"cds_start": 2303,
"cds_end": null,
"cds_length": 3867,
"cdna_start": 2396,
"cdna_end": null,
"cdna_length": 4020,
"mane_select": "ENST00000618853.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPLAH",
"gene_hgnc_id": 8149,
"hgvs_c": "c.2303G>A",
"hgvs_p": "p.Arg768His",
"transcript": "ENST00000618853.5",
"protein_id": "ENSP00000480476.1",
"transcript_support_level": 1,
"aa_start": 768,
"aa_end": null,
"aa_length": 1288,
"cds_start": 2303,
"cds_end": null,
"cds_length": 3867,
"cdna_start": 2396,
"cdna_end": null,
"cdna_length": 4020,
"mane_select": "NM_017570.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPLAH",
"gene_hgnc_id": 8149,
"hgvs_c": "c.2591G>A",
"hgvs_p": "p.Arg864His",
"transcript": "XM_047421688.1",
"protein_id": "XP_047277644.1",
"transcript_support_level": null,
"aa_start": 864,
"aa_end": null,
"aa_length": 1389,
"cds_start": 2591,
"cds_end": null,
"cds_length": 4170,
"cdna_start": 2618,
"cdna_end": null,
"cdna_length": 4289,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPLAH",
"gene_hgnc_id": 8149,
"hgvs_c": "c.2582G>A",
"hgvs_p": "p.Arg861His",
"transcript": "XM_047421689.1",
"protein_id": "XP_047277645.1",
"transcript_support_level": null,
"aa_start": 861,
"aa_end": null,
"aa_length": 1386,
"cds_start": 2582,
"cds_end": null,
"cds_length": 4161,
"cdna_start": 2609,
"cdna_end": null,
"cdna_length": 4280,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPLAH",
"gene_hgnc_id": 8149,
"hgvs_c": "c.2591G>A",
"hgvs_p": "p.Arg864His",
"transcript": "XM_011516960.2",
"protein_id": "XP_011515262.1",
"transcript_support_level": null,
"aa_start": 864,
"aa_end": null,
"aa_length": 1384,
"cds_start": 2591,
"cds_end": null,
"cds_length": 4155,
"cdna_start": 2618,
"cdna_end": null,
"cdna_length": 4242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPLAH",
"gene_hgnc_id": 8149,
"hgvs_c": "c.2303G>A",
"hgvs_p": "p.Arg768His",
"transcript": "XM_047421690.1",
"protein_id": "XP_047277646.1",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 1293,
"cds_start": 2303,
"cds_end": null,
"cds_length": 3882,
"cdna_start": 2396,
"cdna_end": null,
"cdna_length": 4066,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPLAH",
"gene_hgnc_id": 8149,
"hgvs_c": "c.2303G>A",
"hgvs_p": "p.Arg768His",
"transcript": "XM_047421691.1",
"protein_id": "XP_047277647.1",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 1293,
"cds_start": 2303,
"cds_end": null,
"cds_length": 3882,
"cdna_start": 2387,
"cdna_end": null,
"cdna_length": 4058,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPLAH",
"gene_hgnc_id": 8149,
"hgvs_c": "c.2303G>A",
"hgvs_p": "p.Arg768His",
"transcript": "XM_047421692.1",
"protein_id": "XP_047277648.1",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 1288,
"cds_start": 2303,
"cds_end": null,
"cds_length": 3867,
"cdna_start": 2387,
"cdna_end": null,
"cdna_length": 4011,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPLAH",
"gene_hgnc_id": 8149,
"hgvs_c": "c.2586G>A",
"hgvs_p": "p.Ala862Ala",
"transcript": "XM_047421693.1",
"protein_id": "XP_047277649.1",
"transcript_support_level": null,
"aa_start": 862,
"aa_end": null,
"aa_length": 1054,
"cds_start": 2586,
"cds_end": null,
"cds_length": 3165,
"cdna_start": 2613,
"cdna_end": null,
"cdna_length": 3318,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OPLAH",
"gene_hgnc_id": 8149,
"dbsnp": "rs539275646",
"frequency_reference_population": 0.000025236879,
"hom_count_reference_population": 0,
"allele_count_reference_population": 40,
"gnomad_exomes_af": 0.000023032,
"gnomad_genomes_af": 0.0000459951,
"gnomad_exomes_ac": 33,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8092048168182373,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.61,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9709,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.22,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.11,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5_Moderate",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000618853.5",
"gene_symbol": "OPLAH",
"hgnc_id": 8149,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2303G>A",
"hgvs_p": "p.Arg768His"
}
],
"clinvar_disease": "5-Oxoprolinase deficiency,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:2",
"phenotype_combined": "not provided|5-Oxoprolinase deficiency",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}