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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: 13-99970413-TGGCGGCGGCGGCGGCGGCGGC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=99970413&ref=TGGCGGCGGCGGCGGCGGCGGC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 99970413,
"ref": "TGGCGGCGGCGGCGGCGGCGGC",
"alt": "T",
"effect": "disruptive_inframe_deletion",
"transcript": "NM_033132.5",
"consequences": [
{
"aa_ref": "PPPPPPPP",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC5",
"gene_hgnc_id": 20322,
"hgvs_c": "c.1170_1190delGCCGCCGCCGCCGCCGCCGCC",
"hgvs_p": "p.Pro391_Pro397del",
"transcript": "NM_033132.5",
"protein_id": "NP_149123.3",
"transcript_support_level": null,
"aa_start": 390,
"aa_end": null,
"aa_length": 639,
"cds_start": 1170,
"cds_end": null,
"cds_length": 1920,
"cdna_start": 1354,
"cdna_end": null,
"cdna_length": 4497,
"mane_select": "ENST00000267294.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "PPPPPPPP",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC5",
"gene_hgnc_id": 20322,
"hgvs_c": "c.1170_1190delGCCGCCGCCGCCGCCGCCGCC",
"hgvs_p": "p.Pro391_Pro397del",
"transcript": "ENST00000267294.5",
"protein_id": "ENSP00000267294.4",
"transcript_support_level": 1,
"aa_start": 390,
"aa_end": null,
"aa_length": 639,
"cds_start": 1170,
"cds_end": null,
"cds_length": 1920,
"cdna_start": 1354,
"cdna_end": null,
"cdna_length": 4497,
"mane_select": "NM_033132.5",
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC5",
"gene_hgnc_id": 20322,
"hgvs_c": "n.1476_1496delGCCGCCGCCGCCGCCGCCGCC",
"hgvs_p": null,
"transcript": "NR_146224.1",
"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": 4800,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000297638",
"gene_hgnc_id": null,
"hgvs_c": "n.135+301_135+321delGGCGGCGGCGGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000749511.1",
"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": 1192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000297638",
"gene_hgnc_id": null,
"hgvs_c": "n.104+295_104+315delGGCGGCGGCGGCGGCGGCGGC",
"hgvs_p": null,
"transcript": "ENST00000749512.1",
"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": 1161,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ZIC5",
"gene_hgnc_id": 20322,
"dbsnp": "rs71114653",
"frequency_reference_population": 0.008667679,
"hom_count_reference_population": 1781,
"allele_count_reference_population": 9592,
"gnomad_exomes_af": 0.00909237,
"gnomad_genomes_af": 0.00524255,
"gnomad_exomes_ac": 8952,
"gnomad_genomes_ac": 640,
"gnomad_exomes_homalt": 1778,
"gnomad_genomes_homalt": 3,
"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": 2.556,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP3,BP6_Moderate,BS1,BS2",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP3",
"BP6_Moderate",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_033132.5",
"gene_symbol": "ZIC5",
"hgnc_id": 20322,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1170_1190delGCCGCCGCCGCCGCCGCCGCC",
"hgvs_p": "p.Pro391_Pro397del"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP6_Moderate",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000749511.1",
"gene_symbol": "ENSG00000297638",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.135+301_135+321delGGCGGCGGCGGCGGCGGCGGC",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}