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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: 12-40225280-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=40225280&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 40225280,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000298910.12",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His",
"transcript": "NM_198578.4",
"protein_id": "NP_940980.4",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 2527,
"cds_start": 149,
"cds_end": null,
"cds_length": 7584,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 9239,
"mane_select": "ENST00000298910.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His",
"transcript": "ENST00000298910.12",
"protein_id": "ENSP00000298910.7",
"transcript_support_level": 1,
"aa_start": 50,
"aa_end": null,
"aa_length": 2527,
"cds_start": 149,
"cds_end": null,
"cds_length": 7584,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 9239,
"mane_select": "NM_198578.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His",
"transcript": "ENST00000680790.1",
"protein_id": "ENSP00000505335.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 2442,
"cds_start": 149,
"cds_end": null,
"cds_length": 7329,
"cdna_start": 201,
"cdna_end": null,
"cdna_length": 8875,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His",
"transcript": "ENST00000343742.6",
"protein_id": "ENSP00000341930.2",
"transcript_support_level": 5,
"aa_start": 50,
"aa_end": null,
"aa_length": 1271,
"cds_start": 149,
"cds_end": null,
"cds_length": 3816,
"cdna_start": 270,
"cdna_end": null,
"cdna_length": 4740,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His",
"transcript": "XM_005268629.5",
"protein_id": "XP_005268686.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 2521,
"cds_start": 149,
"cds_end": null,
"cds_length": 7566,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 9221,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His",
"transcript": "XM_011537877.4",
"protein_id": "XP_011536179.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 2503,
"cds_start": 149,
"cds_end": null,
"cds_length": 7512,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 9167,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His",
"transcript": "XM_047428277.1",
"protein_id": "XP_047284233.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 2490,
"cds_start": 149,
"cds_end": null,
"cds_length": 7473,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 10778,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His",
"transcript": "XM_047428278.1",
"protein_id": "XP_047284234.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 2371,
"cds_start": 149,
"cds_end": null,
"cds_length": 7116,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 10600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His",
"transcript": "XM_047428279.1",
"protein_id": "XP_047284235.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 1621,
"cds_start": 149,
"cds_end": null,
"cds_length": 4866,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 8660,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His",
"transcript": "XM_011537881.4",
"protein_id": "XP_011536183.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 1611,
"cds_start": 149,
"cds_end": null,
"cds_length": 4836,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 5117,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His",
"transcript": "XM_017018786.3",
"protein_id": "XP_016874275.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 1524,
"cds_start": 149,
"cds_end": null,
"cds_length": 4575,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 4761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His",
"transcript": "XM_011537882.4",
"protein_id": "XP_011536184.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 1271,
"cds_start": 149,
"cds_end": null,
"cds_length": 3816,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 4107,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.92G>A",
"hgvs_p": null,
"transcript": "ENST00000644108.1",
"protein_id": "ENSP00000493752.1",
"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": 1151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.149G>A",
"hgvs_p": null,
"transcript": "ENST00000679360.1",
"protein_id": "ENSP00000505368.1",
"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": 7718,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.304G>A",
"hgvs_p": null,
"transcript": "ENST00000680235.1",
"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": 2344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.284G>A",
"hgvs_p": null,
"transcript": "XR_007063041.1",
"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": 11176,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.-62-275G>A",
"hgvs_p": null,
"transcript": "ENST00000416796.5",
"protein_id": "ENSP00000398726.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 520,
"cds_start": -4,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"dbsnp": "rs2256408",
"frequency_reference_population": 0.9947927,
"hom_count_reference_population": 799029,
"allele_count_reference_population": 1605673,
"gnomad_exomes_af": 0.997162,
"gnomad_genomes_af": 0.972043,
"gnomad_exomes_ac": 1457662,
"gnomad_genomes_ac": 148011,
"gnomad_exomes_homalt": 726959,
"gnomad_genomes_homalt": 72070,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 8.56998610743176e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.029,
"revel_prediction": "Benign",
"alphamissense_score": 0.0615,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.216,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000404243866858565,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000298910.12",
"gene_symbol": "LRRK2",
"hgnc_id": 18618,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50His"
}
],
"clinvar_disease": "Autosomal dominant Parkinson disease 8,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "Autosomal dominant Parkinson disease 8|not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}