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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: 6-52236959-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=52236959&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 52236959,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_052872.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL17F",
"gene_hgnc_id": 16404,
"hgvs_c": "c.464T>G",
"hgvs_p": "p.Val155Gly",
"transcript": "NM_052872.4",
"protein_id": "NP_443104.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 163,
"cds_start": 464,
"cds_end": null,
"cds_length": 492,
"cdna_start": 535,
"cdna_end": null,
"cdna_length": 813,
"mane_select": "ENST00000336123.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL17F",
"gene_hgnc_id": 16404,
"hgvs_c": "c.464T>G",
"hgvs_p": "p.Val155Gly",
"transcript": "ENST00000336123.5",
"protein_id": "ENSP00000337432.4",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 163,
"cds_start": 464,
"cds_end": null,
"cds_length": 492,
"cdna_start": 535,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL17F",
"gene_hgnc_id": 16404,
"hgvs_c": "n.648T>G",
"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": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL17F",
"gene_hgnc_id": 16404,
"hgvs_c": "c.464T>G",
"hgvs_p": "p.Val155Gly",
"transcript": "ENST00000699946.1",
"protein_id": "ENSP00000514702.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 163,
"cds_start": 464,
"cds_end": null,
"cds_length": 492,
"cdna_start": 601,
"cdna_end": null,
"cdna_length": 879,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL17F",
"gene_hgnc_id": 16404,
"hgvs_c": "c.464T>G",
"hgvs_p": "p.Val155Gly",
"transcript": "XM_011514276.1",
"protein_id": "XP_011512578.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 163,
"cds_start": 464,
"cds_end": null,
"cds_length": 492,
"cdna_start": 601,
"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": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124901328",
"gene_hgnc_id": null,
"hgvs_c": "n.-127A>C",
"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": "rs746053425",
"frequency_reference_population": 0.0000088933275,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000889333,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9452552795410156,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.68,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7592,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.25,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.589,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,BS2",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 4,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_052872.4",
"gene_symbol": "IL17F",
"hgnc_id": 16404,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.464T>G",
"hgvs_p": "p.Val155Gly"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "XR_007059607.1",
"gene_symbol": "LOC124901328",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-127A>C",
"hgvs_p": null
}
],
"clinvar_disease": " 6, familial,Candidiasis",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Candidiasis, familial, 6",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}