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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-137566825-ACGCCGCCGC-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=137566825&ref=ACGCCGCCGC&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 137566825,
"ref": "ACGCCGCCGC",
"alt": "A",
"effect": "disruptive_inframe_deletion",
"transcript": "ENST00000287538.10",
"consequences": [
{
"aa_ref": "AAAA",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC3",
"gene_hgnc_id": 12874,
"hgvs_c": "c.153_161delCGCCGCCGC",
"hgvs_p": "p.Ala52_Ala54del",
"transcript": "NM_003413.4",
"protein_id": "NP_003404.1",
"transcript_support_level": null,
"aa_start": 51,
"aa_end": null,
"aa_length": 467,
"cds_start": 153,
"cds_end": null,
"cds_length": 1404,
"cdna_start": 718,
"cdna_end": null,
"cdna_length": 4001,
"mane_select": "ENST00000287538.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AAAA",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC3",
"gene_hgnc_id": 12874,
"hgvs_c": "c.153_161delCGCCGCCGC",
"hgvs_p": "p.Ala52_Ala54del",
"transcript": "ENST00000287538.10",
"protein_id": "ENSP00000287538.5",
"transcript_support_level": 1,
"aa_start": 51,
"aa_end": null,
"aa_length": 467,
"cds_start": 153,
"cds_end": null,
"cds_length": 1404,
"cdna_start": 718,
"cdna_end": null,
"cdna_length": 4001,
"mane_select": "NM_003413.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AAAA",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC3",
"gene_hgnc_id": 12874,
"hgvs_c": "c.153_161delCGCCGCCGC",
"hgvs_p": "p.Ala52_Ala54del",
"transcript": "NM_001330661.1",
"protein_id": "NP_001317590.1",
"transcript_support_level": null,
"aa_start": 51,
"aa_end": null,
"aa_length": 457,
"cds_start": 153,
"cds_end": null,
"cds_length": 1374,
"cdna_start": 718,
"cdna_end": null,
"cdna_length": 2359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AAAA",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC3",
"gene_hgnc_id": 12874,
"hgvs_c": "c.153_161delCGCCGCCGC",
"hgvs_p": "p.Ala52_Ala54del",
"transcript": "ENST00000370606.3",
"protein_id": "ENSP00000359638.3",
"transcript_support_level": 5,
"aa_start": 51,
"aa_end": null,
"aa_length": 457,
"cds_start": 153,
"cds_end": null,
"cds_length": 1374,
"cdna_start": 327,
"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": 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+2240_130+2248delGCGGCGGCG",
"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": "rs748325646",
"frequency_reference_population": 0.00066944095,
"hom_count_reference_population": 230,
"allele_count_reference_population": 777,
"gnomad_exomes_af": 0.000663572,
"gnomad_genomes_af": 0.000724502,
"gnomad_exomes_ac": 696,
"gnomad_genomes_ac": 81,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.405,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP3,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP3",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000287538.10",
"gene_symbol": "ZIC3",
"hgnc_id": 12874,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "XL",
"hgvs_c": "c.153_161delCGCCGCCGC",
"hgvs_p": "p.Ala52_Ala54del"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP6_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000786828.1",
"gene_symbol": "LINC02931",
"hgnc_id": 55853,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.130+2240_130+2248delGCGGCGGCG",
"hgvs_p": null
}
],
"clinvar_disease": " 1, X-linked, visceral,Heterotaxy,ZIC3-related disorder,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "not provided|Heterotaxy, visceral, 1, X-linked|ZIC3-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}