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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: 2-128268254-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=128268254&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 128268254,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000259241.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST1",
"gene_hgnc_id": 5201,
"hgvs_c": "c.1144C>T",
"hgvs_p": "p.Arg382Trp",
"transcript": "NM_004807.3",
"protein_id": "NP_004798.3",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 411,
"cds_start": 1144,
"cds_end": null,
"cds_length": 1236,
"cdna_start": 1449,
"cdna_end": null,
"cdna_length": 4223,
"mane_select": "ENST00000259241.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST1",
"gene_hgnc_id": 5201,
"hgvs_c": "c.1144C>T",
"hgvs_p": "p.Arg382Trp",
"transcript": "ENST00000259241.7",
"protein_id": "ENSP00000259241.6",
"transcript_support_level": 1,
"aa_start": 382,
"aa_end": null,
"aa_length": 411,
"cds_start": 1144,
"cds_end": null,
"cds_length": 1236,
"cdna_start": 1449,
"cdna_end": null,
"cdna_length": 4223,
"mane_select": "NM_004807.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HS6ST1",
"gene_hgnc_id": 5201,
"hgvs_c": "n.361-21729C>T",
"hgvs_p": null,
"transcript": "ENST00000469019.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HS6ST1",
"gene_hgnc_id": 5201,
"dbsnp": "rs199538589",
"frequency_reference_population": 0.0011951628,
"hom_count_reference_population": 21,
"allele_count_reference_population": 1926,
"gnomad_exomes_af": 0.00121574,
"gnomad_genomes_af": 0.000998043,
"gnomad_exomes_ac": 1774,
"gnomad_genomes_ac": 152,
"gnomad_exomes_homalt": 19,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01863241195678711,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.634,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.292,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.539,
"phylop100way_prediction": "Uncertain_significance",
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000259241.7",
"gene_symbol": "HS6ST1",
"hgnc_id": 5201,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AD",
"hgvs_c": "c.1144C>T",
"hgvs_p": "p.Arg382Trp"
}
],
"clinvar_disease": " SUSCEPTIBILITY TO,HS6ST1-related disorder,HYPOGONADOTROPIC HYPOGONADISM 15 WITH OR WITHOUT ANOSMIA,Hypogonadotropic hypogonadism 15 with or without anosmia,Hypogonadotropic hypogonadism 7 with or without anosmia,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:1 US:1 LB:1 B:4",
"phenotype_combined": "HYPOGONADOTROPIC HYPOGONADISM 15 WITH OR WITHOUT ANOSMIA, SUSCEPTIBILITY TO|Hypogonadotropic hypogonadism 7 with or without anosmia|not specified|not provided|Hypogonadotropic hypogonadism 15 with or without anosmia|HS6ST1-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}