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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: 15-43234829-ACTGC-TGAAGGA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=43234829&ref=ACTGC&alt=TGAAGGA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 43234829,
"ref": "ACTGC",
"alt": "TGAAGGA",
"effect": "frameshift_variant,missense_variant",
"transcript": "ENST00000220420.10",
"consequences": [
{
"aa_ref": "SS",
"aa_alt": "IL?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGM5",
"gene_hgnc_id": 11781,
"hgvs_c": "c.1811_1815delGCAGTinsTCCTTCA",
"hgvs_p": "p.Ser604fs",
"transcript": "NM_201631.4",
"protein_id": "NP_963925.2",
"transcript_support_level": null,
"aa_start": 604,
"aa_end": null,
"aa_length": 720,
"cds_start": 1811,
"cds_end": null,
"cds_length": 2163,
"cdna_start": 1894,
"cdna_end": null,
"cdna_length": 2843,
"mane_select": "ENST00000220420.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "IL?",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGM5",
"gene_hgnc_id": 11781,
"hgvs_c": "c.1811_1815delGCAGTinsTCCTTCA",
"hgvs_p": "p.Ser604fs",
"transcript": "ENST00000220420.10",
"protein_id": "ENSP00000220420.5",
"transcript_support_level": 1,
"aa_start": 604,
"aa_end": null,
"aa_length": 720,
"cds_start": 1811,
"cds_end": null,
"cds_length": 2163,
"cdna_start": 1894,
"cdna_end": null,
"cdna_length": 2843,
"mane_select": "NM_201631.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "IL?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGM5",
"gene_hgnc_id": 11781,
"hgvs_c": "c.1565_1569delGCAGTinsTCCTTCA",
"hgvs_p": "p.Ser522fs",
"transcript": "ENST00000349114.8",
"protein_id": "ENSP00000220419.8",
"transcript_support_level": 1,
"aa_start": 522,
"aa_end": null,
"aa_length": 638,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1917,
"cdna_start": 1577,
"cdna_end": null,
"cdna_length": 1958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "IL?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGM5",
"gene_hgnc_id": 11781,
"hgvs_c": "c.1565_1569delGCAGTinsTCCTTCA",
"hgvs_p": "p.Ser522fs",
"transcript": "NM_004245.4",
"protein_id": "NP_004236.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 638,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1917,
"cdna_start": 1648,
"cdna_end": null,
"cdna_length": 2597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "IL?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGM5",
"gene_hgnc_id": 11781,
"hgvs_c": "c.782_786delGCAGTinsTCCTTCA",
"hgvs_p": "p.Ser261fs",
"transcript": "XM_011522230.3",
"protein_id": "XP_011520532.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 377,
"cds_start": 782,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 1018,
"cdna_end": null,
"cdna_length": 1967,
"mane_select": null,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGM5",
"gene_hgnc_id": 11781,
"hgvs_c": "n.1287_1291delGCAGTinsTCCTTCA",
"hgvs_p": null,
"transcript": "ENST00000396996.3",
"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": 1653,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TGM5",
"gene_hgnc_id": 11781,
"dbsnp": "rs606231278",
"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": 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": 1.836,
"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": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000220420.10",
"gene_symbol": "TGM5",
"hgnc_id": 11781,
"effects": [
"frameshift_variant",
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1811_1815delGCAGTinsTCCTTCA",
"hgvs_p": "p.Ser604fs"
}
],
"clinvar_disease": "Acral peeling skin syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Acral peeling skin syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}