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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: 6-52238729-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=52238729&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 52238729,
"ref": "C",
"alt": "T",
"effect": "splice_donor_variant,intron_variant",
"transcript": "ENST00000336123.5",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "IL17F",
"gene_hgnc_id": 16404,
"hgvs_c": "c.254+1G>A",
"hgvs_p": null,
"transcript": "NM_052872.4",
"protein_id": "NP_443104.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 163,
"cds_start": -4,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 813,
"mane_select": "ENST00000336123.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "IL17F",
"gene_hgnc_id": 16404,
"hgvs_c": "c.254+1G>A",
"hgvs_p": null,
"transcript": "ENST00000336123.5",
"protein_id": "ENSP00000337432.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 163,
"cds_start": -4,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 813,
"mane_select": "NM_052872.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IL17F",
"gene_hgnc_id": 16404,
"hgvs_c": "n.438+1G>A",
"hgvs_p": null,
"transcript": "ENST00000478427.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 926,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "IL17F",
"gene_hgnc_id": 16404,
"hgvs_c": "c.254+1G>A",
"hgvs_p": null,
"transcript": "ENST00000699946.1",
"protein_id": "ENSP00000514702.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 163,
"cds_start": -4,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 879,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "IL17F",
"gene_hgnc_id": 16404,
"hgvs_c": "c.254+1G>A",
"hgvs_p": null,
"transcript": "XM_011514276.1",
"protein_id": "XP_011512578.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 163,
"cds_start": -4,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 879,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC124901328",
"gene_hgnc_id": null,
"hgvs_c": "n.251-13C>T",
"hgvs_p": null,
"transcript": "XR_007059607.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 332,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IL17F",
"gene_hgnc_id": 16404,
"dbsnp": "rs117796773",
"frequency_reference_population": 0.00006017855,
"hom_count_reference_population": 0,
"allele_count_reference_population": 97,
"gnomad_exomes_af": 0.0000637124,
"gnomad_genomes_af": 0.0000262836,
"gnomad_exomes_ac": 93,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.38999998569488525,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9380000233650208,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.39,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.509,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.92,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999990361384395,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP6,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000336123.5",
"gene_symbol": "IL17F",
"hgnc_id": 16404,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.254+1G>A",
"hgvs_p": null
},
{
"score": 5,
"benign_score": 1,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007059607.1",
"gene_symbol": "LOC124901328",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.251-13C>T",
"hgvs_p": null
}
],
"clinvar_disease": " 6, familial,Candidiasis",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 B:1",
"phenotype_combined": "Candidiasis, familial, 6",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}