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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: X-129814794-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=129814794&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 129814794,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "ENST00000357166.11",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC9",
"gene_hgnc_id": 18475,
"hgvs_c": "c.489G>A",
"hgvs_p": "p.Glu163Glu",
"transcript": "NM_016032.4",
"protein_id": "NP_057116.2",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 364,
"cds_start": 489,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 883,
"cdna_end": null,
"cdna_length": 4571,
"mane_select": "ENST00000357166.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC9",
"gene_hgnc_id": 18475,
"hgvs_c": "c.489G>A",
"hgvs_p": "p.Glu163Glu",
"transcript": "ENST00000357166.11",
"protein_id": "ENSP00000349689.6",
"transcript_support_level": 1,
"aa_start": 163,
"aa_end": null,
"aa_length": 364,
"cds_start": 489,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 883,
"cdna_end": null,
"cdna_length": 4571,
"mane_select": "NM_016032.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC9",
"gene_hgnc_id": 18475,
"hgvs_c": "c.489G>A",
"hgvs_p": "p.Glu163Glu",
"transcript": "ENST00000371064.7",
"protein_id": "ENSP00000360103.3",
"transcript_support_level": 1,
"aa_start": 163,
"aa_end": null,
"aa_length": 364,
"cds_start": 489,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 826,
"cdna_end": null,
"cdna_length": 2473,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC9",
"gene_hgnc_id": 18475,
"hgvs_c": "c.489G>A",
"hgvs_p": "p.Glu163Glu",
"transcript": "NM_001008222.3",
"protein_id": "NP_001008223.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 364,
"cds_start": 489,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 965,
"cdna_end": null,
"cdna_length": 4653,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC9",
"gene_hgnc_id": 18475,
"hgvs_c": "c.489G>A",
"hgvs_p": "p.Glu163Glu",
"transcript": "ENST00000406492.2",
"protein_id": "ENSP00000383991.2",
"transcript_support_level": 5,
"aa_start": 163,
"aa_end": null,
"aa_length": 169,
"cds_start": 489,
"cds_end": null,
"cds_length": 512,
"cdna_start": 714,
"cdna_end": null,
"cdna_length": 737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC9",
"gene_hgnc_id": 18475,
"hgvs_c": "c.489G>A",
"hgvs_p": "p.Glu163Glu",
"transcript": "XM_047442151.1",
"protein_id": "XP_047298107.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 235,
"cds_start": 489,
"cds_end": null,
"cds_length": 708,
"cdna_start": 883,
"cdna_end": null,
"cdna_length": 1281,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ZDHHC9",
"gene_hgnc_id": 18475,
"hgvs_c": "c.365-1069G>A",
"hgvs_p": null,
"transcript": "ENST00000433917.5",
"protein_id": "ENSP00000406165.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 192,
"cds_start": -4,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ZDHHC9",
"gene_hgnc_id": 18475,
"dbsnp": "rs1339214564",
"frequency_reference_population": 0.0000016538548,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 9.10771e-7,
"gnomad_genomes_af": 0.00000898271,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.36000001430511475,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.927,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000679107076424536,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000357166.11",
"gene_symbol": "ZDHHC9",
"hgnc_id": 18475,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.489G>A",
"hgvs_p": "p.Glu163Glu"
}
],
"clinvar_disease": "Syndromic X-linked intellectual disability Raymond type",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Syndromic X-linked intellectual disability Raymond type",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}