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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: 19-54128343-TCCGGAAGCAGG-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=54128343&ref=TCCGGAAGCAGG&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 54128343,
"ref": "TCCGGAAGCAGG",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "ENST00000321030.9",
"consequences": [
{
"aa_ref": "RKQA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPF31",
"gene_hgnc_id": 15446,
"hgvs_c": "c.1115_1125delGGAAGCAGGCC",
"hgvs_p": "p.Arg372fs",
"transcript": "NM_015629.4",
"protein_id": "NP_056444.3",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 499,
"cds_start": 1115,
"cds_end": null,
"cds_length": 1500,
"cdna_start": 1167,
"cdna_end": null,
"cdna_length": 1833,
"mane_select": "ENST00000321030.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "RKQA",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPF31",
"gene_hgnc_id": 15446,
"hgvs_c": "c.1115_1125delGGAAGCAGGCC",
"hgvs_p": "p.Arg372fs",
"transcript": "ENST00000321030.9",
"protein_id": "ENSP00000324122.4",
"transcript_support_level": 1,
"aa_start": 372,
"aa_end": null,
"aa_length": 499,
"cds_start": 1115,
"cds_end": null,
"cds_length": 1500,
"cdna_start": 1167,
"cdna_end": null,
"cdna_length": 1833,
"mane_select": "NM_015629.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "RKQA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPF31",
"gene_hgnc_id": 15446,
"hgvs_c": "c.1097_1107delGGAAGCAGGCC",
"hgvs_p": "p.Arg366fs",
"transcript": "ENST00000391755.1",
"protein_id": "ENSP00000375635.1",
"transcript_support_level": 5,
"aa_start": 366,
"aa_end": null,
"aa_length": 493,
"cds_start": 1097,
"cds_end": null,
"cds_length": 1482,
"cdna_start": 1105,
"cdna_end": null,
"cdna_length": 1767,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "RKQA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPF31",
"gene_hgnc_id": 15446,
"hgvs_c": "c.1115_1125delGGAAGCAGGCC",
"hgvs_p": "p.Arg372fs",
"transcript": "ENST00000419967.5",
"protein_id": "ENSP00000405166.2",
"transcript_support_level": 5,
"aa_start": 372,
"aa_end": null,
"aa_length": 491,
"cds_start": 1115,
"cds_end": null,
"cds_length": 1476,
"cdna_start": 1511,
"cdna_end": null,
"cdna_length": 2269,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "RKQA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPF31",
"gene_hgnc_id": 15446,
"hgvs_c": "c.1115_1125delGGAAGCAGGCC",
"hgvs_p": "p.Arg372fs",
"transcript": "XM_006723137.5",
"protein_id": "XP_006723200.1",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 499,
"cds_start": 1115,
"cds_end": null,
"cds_length": 1500,
"cdna_start": 1197,
"cdna_end": null,
"cdna_length": 1863,
"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": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPF31",
"gene_hgnc_id": 15446,
"hgvs_c": "n.1089_1099delGGAAGCAGGCC",
"hgvs_p": null,
"transcript": "ENST00000466404.5",
"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": 1837,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPF31",
"gene_hgnc_id": 15446,
"hgvs_c": "n.*147_*157delCCGGAAGCAGG",
"hgvs_p": null,
"transcript": "ENST00000498612.1",
"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": 881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPF31",
"gene_hgnc_id": 15446,
"hgvs_c": "c.*249_*259delCCGGAAGCAGG",
"hgvs_p": null,
"transcript": "XM_047438587.1",
"protein_id": "XP_047294543.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 331,
"cds_start": -4,
"cds_end": null,
"cds_length": 996,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1148,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRPF31",
"gene_hgnc_id": 15446,
"dbsnp": "rs587776589",
"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": 9.229,
"phylop100way_prediction": "Pathogenic",
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1,PP5",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PVS1",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000321030.9",
"gene_symbol": "PRPF31",
"hgnc_id": 15446,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1115_1125delGGAAGCAGGCC",
"hgvs_p": "p.Arg372fs"
}
],
"clinvar_disease": "Retinitis pigmentosa 11",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Retinitis pigmentosa 11",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}