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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-137568910-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=137568910&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 137568910,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000287538.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC3",
"gene_hgnc_id": 12874,
"hgvs_c": "c.1069C>A",
"hgvs_p": "p.Pro357Thr",
"transcript": "NM_003413.4",
"protein_id": "NP_003404.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 467,
"cds_start": 1069,
"cds_end": null,
"cds_length": 1404,
"cdna_start": 1634,
"cdna_end": null,
"cdna_length": 4001,
"mane_select": "ENST00000287538.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC3",
"gene_hgnc_id": 12874,
"hgvs_c": "c.1069C>A",
"hgvs_p": "p.Pro357Thr",
"transcript": "ENST00000287538.10",
"protein_id": "ENSP00000287538.5",
"transcript_support_level": 1,
"aa_start": 357,
"aa_end": null,
"aa_length": 467,
"cds_start": 1069,
"cds_end": null,
"cds_length": 1404,
"cdna_start": 1634,
"cdna_end": null,
"cdna_length": 4001,
"mane_select": "NM_003413.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC3",
"gene_hgnc_id": 12874,
"hgvs_c": "c.1069C>A",
"hgvs_p": "p.Pro357Thr",
"transcript": "NM_001330661.1",
"protein_id": "NP_001317590.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 457,
"cds_start": 1069,
"cds_end": null,
"cds_length": 1374,
"cdna_start": 1634,
"cdna_end": null,
"cdna_length": 2359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC3",
"gene_hgnc_id": 12874,
"hgvs_c": "c.1069C>A",
"hgvs_p": "p.Pro357Thr",
"transcript": "ENST00000370606.3",
"protein_id": "ENSP00000359638.3",
"transcript_support_level": 5,
"aa_start": 357,
"aa_end": null,
"aa_length": 457,
"cds_start": 1069,
"cds_end": null,
"cds_length": 1374,
"cdna_start": 1243,
"cdna_end": null,
"cdna_length": 1968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC3",
"gene_hgnc_id": 12874,
"hgvs_c": "n.106C>A",
"hgvs_p": null,
"transcript": "ENST00000478471.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 366,
"mane_select": null,
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LINC02931",
"gene_hgnc_id": 55853,
"hgvs_c": "n.130+164G>T",
"hgvs_p": null,
"transcript": "ENST00000786828.1",
"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": 1476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ZIC3",
"gene_hgnc_id": 12874,
"dbsnp": "rs1556030199",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9170816540718079,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.57,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9848,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.15,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.85,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000287538.10",
"gene_symbol": "ZIC3",
"hgnc_id": 12874,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1069C>A",
"hgvs_p": "p.Pro357Thr"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000786828.1",
"gene_symbol": "LINC02931",
"hgnc_id": 55853,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.130+164G>T",
"hgvs_p": null
}
],
"clinvar_disease": " 1, X-linked, visceral,Heterotaxy",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Heterotaxy, visceral, 1, X-linked",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}