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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: 1-20648577-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=20648577&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PP3_Moderate",
"PP5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PINK1",
"hgnc_id": 14581,
"hgvs_c": "c.1196C>T",
"hgvs_p": "p.Pro399Leu",
"inheritance_mode": "AR,AD",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_032409.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "PINK1-AS",
"hgnc_id": 38872,
"hgvs_c": "n.3617G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 5,
"score": 5,
"transcript": "ENST00000451424.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate,PP5",
"acmg_score": 3,
"allele_count_reference_population": 14,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.2834,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.19,
"chr": "1",
"clinvar_classification": "Pathogenic",
"clinvar_disease": " PINK1/DJ1, autosomal recessive early-onset, digenic,Parkinson disease",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.909109354019165,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 581,
"aa_ref": "P",
"aa_start": 399,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2657,
"cdna_start": 1287,
"cds_end": null,
"cds_length": 1746,
"cds_start": 1196,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_032409.3",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1196C>T",
"hgvs_p": "p.Pro399Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000321556.5",
"protein_coding": true,
"protein_id": "NP_115785.1",
"strand": true,
"transcript": "NM_032409.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 581,
"aa_ref": "P",
"aa_start": 399,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2657,
"cdna_start": 1287,
"cds_end": null,
"cds_length": 1746,
"cds_start": 1196,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000321556.5",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1196C>T",
"hgvs_p": "p.Pro399Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_032409.3",
"protein_coding": true,
"protein_id": "ENSP00000364204.3",
"strand": true,
"transcript": "ENST00000321556.5",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 591,
"aa_ref": "P",
"aa_start": 399,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2429,
"cdna_start": 1223,
"cds_end": null,
"cds_length": 1776,
"cds_start": 1196,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000878749.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1196C>T",
"hgvs_p": "p.Pro399Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548808.1",
"strand": true,
"transcript": "ENST00000878749.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 587,
"aa_ref": "P",
"aa_start": 399,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2667,
"cdna_start": 1281,
"cds_end": null,
"cds_length": 1764,
"cds_start": 1196,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000878743.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1196C>T",
"hgvs_p": "p.Pro399Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548802.1",
"strand": true,
"transcript": "ENST00000878743.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 582,
"aa_ref": "P",
"aa_start": 399,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2452,
"cdna_start": 1273,
"cds_end": null,
"cds_length": 1749,
"cds_start": 1196,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000878745.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1196C>T",
"hgvs_p": "p.Pro399Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548804.1",
"strand": true,
"transcript": "ENST00000878745.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 570,
"aa_ref": "P",
"aa_start": 399,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2603,
"cdna_start": 1267,
"cds_end": null,
"cds_length": 1713,
"cds_start": 1196,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000945624.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1196C>T",
"hgvs_p": "p.Pro399Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000615683.1",
"strand": true,
"transcript": "ENST00000945624.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 566,
"aa_ref": "P",
"aa_start": 384,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2612,
"cdna_start": 1242,
"cds_end": null,
"cds_length": 1701,
"cds_start": 1151,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000878739.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1151C>T",
"hgvs_p": "p.Pro384Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548798.1",
"strand": true,
"transcript": "ENST00000878739.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 558,
"aa_ref": "P",
"aa_start": 399,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2376,
"cdna_start": 1269,
"cds_end": null,
"cds_length": 1677,
"cds_start": 1196,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000878746.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1196C>T",
"hgvs_p": "p.Pro399Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548805.1",
"strand": true,
"transcript": "ENST00000878746.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 542,
"aa_ref": "P",
"aa_start": 399,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2539,
"cdna_start": 1287,
"cds_end": null,
"cds_length": 1629,
"cds_start": 1196,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000878740.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1196C>T",
"hgvs_p": "p.Pro399Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548799.1",
"strand": true,
"transcript": "ENST00000878740.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 539,
"aa_ref": "P",
"aa_start": 357,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2285,
"cdna_start": 1109,
"cds_end": null,
"cds_length": 1620,
"cds_start": 1070,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000878748.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1070C>T",
"hgvs_p": "p.Pro357Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548807.1",
"strand": true,
"transcript": "ENST00000878748.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 535,
"aa_ref": "P",
"aa_start": 353,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1725,
"cdna_start": 1129,
"cds_end": null,
"cds_length": 1608,
"cds_start": 1058,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000940632.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1058C>T",
"hgvs_p": "p.Pro353Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610691.1",
"strand": true,
"transcript": "ENST00000940632.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 534,
"aa_ref": "P",
"aa_start": 352,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1734,
"cdna_start": 1137,
"cds_end": null,
"cds_length": 1605,
"cds_start": 1055,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000940631.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1055C>T",
"hgvs_p": "p.Pro352Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610690.1",
"strand": true,
"transcript": "ENST00000940631.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 520,
"aa_ref": "P",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2472,
"cdna_start": 1104,
"cds_end": null,
"cds_length": 1563,
"cds_start": 1013,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000878741.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1013C>T",
"hgvs_p": "p.Pro338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548800.1",
"strand": true,
"transcript": "ENST00000878741.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 517,
"aa_ref": "P",
"aa_start": 335,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2251,
"cdna_start": 1075,
"cds_end": null,
"cds_length": 1554,
"cds_start": 1004,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000878747.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1004C>T",
"hgvs_p": "p.Pro335Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548806.1",
"strand": true,
"transcript": "ENST00000878747.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 502,
"aa_ref": "P",
"aa_start": 399,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2393,
"cdna_start": 1267,
"cds_end": null,
"cds_length": 1509,
"cds_start": 1196,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000878744.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.1196C>T",
"hgvs_p": "p.Pro399Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548803.1",
"strand": true,
"transcript": "ENST00000878744.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 485,
"aa_ref": "P",
"aa_start": 303,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2365,
"cdna_start": 996,
"cds_end": null,
"cds_length": 1458,
"cds_start": 908,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000878742.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "c.908C>T",
"hgvs_p": "p.Pro303Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548801.1",
"strand": true,
"transcript": "ENST00000878742.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1658,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000400490.2",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "n.289C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000400490.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4443,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000451424.1",
"gene_hgnc_id": 38872,
"gene_symbol": "PINK1-AS",
"hgvs_c": "n.3617G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000451424.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3821,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000492302.1",
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"hgvs_c": "n.2284C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000492302.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4443,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NR_046507.1",
"gene_hgnc_id": 38872,
"gene_symbol": "PINK1-AS",
"hgvs_c": "n.3617G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_046507.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs119451946",
"effect": "missense_variant",
"frequency_reference_population": 0.000008673177,
"gene_hgnc_id": 14581,
"gene_symbol": "PINK1",
"gnomad_exomes_ac": 11,
"gnomad_exomes_af": 0.00000752468,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000196959,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Parkinson disease, autosomal recessive early-onset, digenic, PINK1/DJ1",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.063,
"pos": 20648577,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.468,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.03999999910593033,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.04,
"transcript": "NM_032409.3"
}
]
}