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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: 3-125538554-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=125538554&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 125538554,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_022776.5",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSBPL11",
"gene_hgnc_id": 16397,
"hgvs_c": "c.1921T>A",
"hgvs_p": "p.Phe641Ile",
"transcript": "NM_022776.5",
"protein_id": "NP_073613.2",
"transcript_support_level": null,
"aa_start": 641,
"aa_end": null,
"aa_length": 747,
"cds_start": 1921,
"cds_end": null,
"cds_length": 2244,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000296220.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022776.5"
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSBPL11",
"gene_hgnc_id": 16397,
"hgvs_c": "c.1921T>A",
"hgvs_p": "p.Phe641Ile",
"transcript": "ENST00000296220.6",
"protein_id": "ENSP00000296220.5",
"transcript_support_level": 1,
"aa_start": 641,
"aa_end": null,
"aa_length": 747,
"cds_start": 1921,
"cds_end": null,
"cds_length": 2244,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_022776.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000296220.6"
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSBPL11",
"gene_hgnc_id": 16397,
"hgvs_c": "c.1918T>A",
"hgvs_p": "p.Phe640Ile",
"transcript": "ENST00000910157.1",
"protein_id": "ENSP00000580216.1",
"transcript_support_level": null,
"aa_start": 640,
"aa_end": null,
"aa_length": 746,
"cds_start": 1918,
"cds_end": null,
"cds_length": 2241,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910157.1"
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSBPL11",
"gene_hgnc_id": 16397,
"hgvs_c": "c.1915T>A",
"hgvs_p": "p.Phe639Ile",
"transcript": "ENST00000931704.1",
"protein_id": "ENSP00000601763.1",
"transcript_support_level": null,
"aa_start": 639,
"aa_end": null,
"aa_length": 745,
"cds_start": 1915,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931704.1"
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSBPL11",
"gene_hgnc_id": 16397,
"hgvs_c": "c.1852T>A",
"hgvs_p": "p.Phe618Ile",
"transcript": "ENST00000931706.1",
"protein_id": "ENSP00000601765.1",
"transcript_support_level": null,
"aa_start": 618,
"aa_end": null,
"aa_length": 724,
"cds_start": 1852,
"cds_end": null,
"cds_length": 2175,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931706.1"
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSBPL11",
"gene_hgnc_id": 16397,
"hgvs_c": "c.1780T>A",
"hgvs_p": "p.Phe594Ile",
"transcript": "ENST00000931705.1",
"protein_id": "ENSP00000601764.1",
"transcript_support_level": null,
"aa_start": 594,
"aa_end": null,
"aa_length": 700,
"cds_start": 1780,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931705.1"
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSBPL11",
"gene_hgnc_id": 16397,
"hgvs_c": "c.1759T>A",
"hgvs_p": "p.Phe587Ile",
"transcript": "ENST00000910155.1",
"protein_id": "ENSP00000580214.1",
"transcript_support_level": null,
"aa_start": 587,
"aa_end": null,
"aa_length": 693,
"cds_start": 1759,
"cds_end": null,
"cds_length": 2082,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910155.1"
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSBPL11",
"gene_hgnc_id": 16397,
"hgvs_c": "c.1744T>A",
"hgvs_p": "p.Phe582Ile",
"transcript": "ENST00000910154.1",
"protein_id": "ENSP00000580213.1",
"transcript_support_level": null,
"aa_start": 582,
"aa_end": null,
"aa_length": 688,
"cds_start": 1744,
"cds_end": null,
"cds_length": 2067,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910154.1"
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSBPL11",
"gene_hgnc_id": 16397,
"hgvs_c": "c.1585T>A",
"hgvs_p": "p.Phe529Ile",
"transcript": "ENST00000953165.1",
"protein_id": "ENSP00000623224.1",
"transcript_support_level": null,
"aa_start": 529,
"aa_end": null,
"aa_length": 635,
"cds_start": 1585,
"cds_end": null,
"cds_length": 1908,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953165.1"
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSBPL11",
"gene_hgnc_id": 16397,
"hgvs_c": "c.244T>A",
"hgvs_p": "p.Phe82Ile",
"transcript": "ENST00000910156.1",
"protein_id": "ENSP00000580215.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 188,
"cds_start": 244,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910156.1"
}
],
"gene_symbol": "OSBPL11",
"gene_hgnc_id": 16397,
"dbsnp": "rs771678595",
"frequency_reference_population": 0.000074967815,
"hom_count_reference_population": 0,
"allele_count_reference_population": 121,
"gnomad_exomes_af": 0.0000779847,
"gnomad_genomes_af": 0.0000459921,
"gnomad_exomes_ac": 114,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8035993576049805,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.311,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8679,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.16,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.123,
"phylop100way_prediction": "Pathogenic",
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_022776.5",
"gene_symbol": "OSBPL11",
"hgnc_id": 16397,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1921T>A",
"hgvs_p": "p.Phe641Ile"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}