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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: 1-113114431-AC-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=113114431&ref=AC&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 113114431,
"ref": "AC",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "ENST00000361127.6",
"consequences": [
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRIG2",
"gene_hgnc_id": 20889,
"hgvs_c": "c.2088delC",
"hgvs_p": "p.Ser697fs",
"transcript": "NM_014813.3",
"protein_id": "NP_055628.1",
"transcript_support_level": null,
"aa_start": 696,
"aa_end": null,
"aa_length": 1065,
"cds_start": 2088,
"cds_end": null,
"cds_length": 3198,
"cdna_start": 2297,
"cdna_end": null,
"cdna_length": 11566,
"mane_select": "ENST00000361127.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRIG2",
"gene_hgnc_id": 20889,
"hgvs_c": "c.2088delC",
"hgvs_p": "p.Ser697fs",
"transcript": "ENST00000361127.6",
"protein_id": "ENSP00000355396.4",
"transcript_support_level": 1,
"aa_start": 696,
"aa_end": null,
"aa_length": 1065,
"cds_start": 2088,
"cds_end": null,
"cds_length": 3198,
"cdna_start": 2297,
"cdna_end": null,
"cdna_length": 11566,
"mane_select": "NM_014813.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRIG2",
"gene_hgnc_id": 20889,
"hgvs_c": "c.1779delC",
"hgvs_p": "p.Ser594fs",
"transcript": "NM_001312686.2",
"protein_id": "NP_001299615.1",
"transcript_support_level": null,
"aa_start": 593,
"aa_end": null,
"aa_length": 962,
"cds_start": 1779,
"cds_end": null,
"cds_length": 2889,
"cdna_start": 2409,
"cdna_end": null,
"cdna_length": 11678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRIG2",
"gene_hgnc_id": 20889,
"hgvs_c": "c.1866delC",
"hgvs_p": "p.Ser623fs",
"transcript": "XM_047435521.1",
"protein_id": "XP_047291477.1",
"transcript_support_level": null,
"aa_start": 622,
"aa_end": null,
"aa_length": 991,
"cds_start": 1866,
"cds_end": null,
"cds_length": 2976,
"cdna_start": 7131,
"cdna_end": null,
"cdna_length": 16400,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRIG2",
"gene_hgnc_id": 20889,
"hgvs_c": "c.1779delC",
"hgvs_p": "p.Ser594fs",
"transcript": "XM_024451227.2",
"protein_id": "XP_024306995.1",
"transcript_support_level": null,
"aa_start": 593,
"aa_end": null,
"aa_length": 962,
"cds_start": 1779,
"cds_end": null,
"cds_length": 2889,
"cdna_start": 2073,
"cdna_end": null,
"cdna_length": 11342,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRIG2",
"gene_hgnc_id": 20889,
"hgvs_c": "c.1767delC",
"hgvs_p": "p.Ser590fs",
"transcript": "XM_005271369.3",
"protein_id": "XP_005271426.1",
"transcript_support_level": null,
"aa_start": 589,
"aa_end": null,
"aa_length": 958,
"cds_start": 1767,
"cds_end": null,
"cds_length": 2877,
"cdna_start": 1976,
"cdna_end": null,
"cdna_length": 11245,
"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": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRIG2",
"gene_hgnc_id": 20889,
"hgvs_c": "n.1360delC",
"hgvs_p": null,
"transcript": "ENST00000466161.1",
"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": 3366,
"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": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRIG2",
"gene_hgnc_id": 20889,
"hgvs_c": "n.867delC",
"hgvs_p": null,
"transcript": "ENST00000492207.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 5076,
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000303525",
"gene_hgnc_id": null,
"hgvs_c": "n.363+15325delG",
"hgvs_p": null,
"transcript": "ENST00000795269.1",
"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": 595,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LRIG2",
"gene_hgnc_id": 20889,
"dbsnp": "rs587776947",
"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": 0.25,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 7.84,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.25,
"spliceai_max_prediction": "Uncertain_significance",
"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": "ENST00000361127.6",
"gene_symbol": "LRIG2",
"hgnc_id": 20889,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2088delC",
"hgvs_p": "p.Ser697fs"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000795269.1",
"gene_symbol": "ENSG00000303525",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.363+15325delG",
"hgvs_p": null
}
],
"clinvar_disease": "Urofacial syndrome 2",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Urofacial syndrome 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}