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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: 12-40323151-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=40323151&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 40323151,
"ref": "A",
"alt": "G",
"effect": "intron_variant",
"transcript": "NM_198578.4",
"consequences": [
{
"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": 51,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5510-9A>G",
"hgvs_p": null,
"transcript": "NM_198578.4",
"protein_id": "NP_940980.4",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2527,
"cds_start": null,
"cds_end": null,
"cds_length": 7584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9239,
"mane_select": "ENST00000298910.12",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_198578.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5510-9A>G",
"hgvs_p": null,
"transcript": "ENST00000298910.12",
"protein_id": "ENSP00000298910.7",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2527,
"cds_start": null,
"cds_end": null,
"cds_length": 7584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9239,
"mane_select": "NM_198578.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000298910.12"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*2183-9A>G",
"hgvs_p": null,
"transcript": "ENST00000430804.5",
"protein_id": "ENSP00000410821.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6400,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000430804.5"
},
{
"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": 51,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5486-9A>G",
"hgvs_p": null,
"transcript": "ENST00000950031.1",
"protein_id": "ENSP00000620090.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2519,
"cds_start": null,
"cds_end": null,
"cds_length": 7560,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8223,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950031.1"
},
{
"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": 49,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5255-9A>G",
"hgvs_p": null,
"transcript": "ENST00000680790.1",
"protein_id": "ENSP00000505335.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2442,
"cds_start": null,
"cds_end": null,
"cds_length": 7329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8875,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680790.1"
},
{
"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": 21,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.1193-9A>G",
"hgvs_p": null,
"transcript": "ENST00000681696.1",
"protein_id": "ENSP00000505871.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1052,
"cds_start": null,
"cds_end": null,
"cds_length": 3159,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3828,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000681696.1"
},
{
"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": 51,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5510-9A>G",
"hgvs_p": null,
"transcript": "XM_005268629.5",
"protein_id": "XP_005268686.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2521,
"cds_start": null,
"cds_end": null,
"cds_length": 7566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9221,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005268629.5"
},
{
"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": 50,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5510-9A>G",
"hgvs_p": null,
"transcript": "XM_011537877.4",
"protein_id": "XP_011536179.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2503,
"cds_start": null,
"cds_end": null,
"cds_length": 7512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9167,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011537877.4"
},
{
"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": 49,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5510-9A>G",
"hgvs_p": null,
"transcript": "XM_047428277.1",
"protein_id": "XP_047284233.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2490,
"cds_start": null,
"cds_end": null,
"cds_length": 7473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10778,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428277.1"
},
{
"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": 48,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5510-9A>G",
"hgvs_p": null,
"transcript": "XM_047428278.1",
"protein_id": "XP_047284234.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2371,
"cds_start": null,
"cds_end": null,
"cds_length": 7116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10600,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428278.1"
},
{
"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": 42,
"intron_rank": 28,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.4307-9A>G",
"hgvs_p": null,
"transcript": "XM_024448833.2",
"protein_id": "XP_024304601.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2126,
"cds_start": null,
"cds_end": null,
"cds_length": 6381,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8403,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024448833.2"
},
{
"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": 30,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.2426-9A>G",
"hgvs_p": null,
"transcript": "XM_017018787.2",
"protein_id": "XP_016874276.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1499,
"cds_start": null,
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"cds_length": 4500,
"cdna_start": null,
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"cdna_length": 6169,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017018787.2"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.2191-9A>G",
"hgvs_p": null,
"transcript": "ENST00000479187.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
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"cds_length": null,
"cdna_start": null,
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"cdna_length": 8306,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000479187.5"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
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],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": 38,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*4419-9A>G",
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"transcript": "ENST00000679360.1",
"protein_id": "ENSP00000505368.1",
"transcript_support_level": null,
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"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000679360.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*770-9A>G",
"hgvs_p": null,
"transcript": "ENST00000679532.1",
"protein_id": "ENSP00000506435.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
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"cdna_start": null,
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"cdna_length": 4852,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000679532.1"
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*733-9A>G",
"hgvs_p": null,
"transcript": "ENST00000680018.1",
"protein_id": "ENSP00000505347.1",
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"mane_select": null,
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000680018.1"
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.1154-9A>G",
"hgvs_p": null,
"transcript": "ENST00000680422.1",
"protein_id": "ENSP00000505304.1",
"transcript_support_level": null,
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"mane_select": null,
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000680422.1"
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*545-9A>G",
"hgvs_p": null,
"transcript": "ENST00000680425.1",
"protein_id": "ENSP00000506459.1",
"transcript_support_level": null,
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"aa_end": null,
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000680425.1"
},
{
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"canonical": false,
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"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 20,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*486-9A>G",
"hgvs_p": null,
"transcript": "ENST00000680453.1",
"protein_id": "ENSP00000505566.1",
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"feature": "ENST00000680453.1"
},
{
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"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
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"exon_count": 21,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.1494-9A>G",
"hgvs_p": null,
"transcript": "ENST00000681136.1",
"protein_id": null,
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"cdna_length": 4081,
"mane_select": null,
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"biotype": "pseudogene",
"feature": "ENST00000681136.1"
},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258167",
"gene_hgnc_id": null,
"hgvs_c": "n.308-732T>C",
"hgvs_p": null,
"transcript": "ENST00000724141.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
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"aa_length": null,
"cds_start": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 720,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000724141.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.5645-9A>G",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11176,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007063041.1"
}
],
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"dbsnp": "rs41286460",
"frequency_reference_population": 0.0031633032,
"hom_count_reference_population": 21,
"allele_count_reference_population": 5094,
"gnomad_exomes_af": 0.00321843,
"gnomad_genomes_af": 0.00263507,
"gnomad_exomes_ac": 4693,
"gnomad_genomes_ac": 401,
"gnomad_exomes_homalt": 19,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8700000047683716,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.87,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.107,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000201357299852055,
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_198578.4",
"gene_symbol": "LRRK2",
"hgnc_id": 18618,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.5510-9A>G",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000724141.1",
"gene_symbol": "ENSG00000258167",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.308-732T>C",
"hgvs_p": null
}
],
"clinvar_disease": " Dominant,Autosomal dominant Parkinson disease 8,LRRK2-related disorder,Parkinson Disease,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:4",
"phenotype_combined": "Parkinson Disease, Dominant|not specified|Autosomal dominant Parkinson disease 8|not provided|LRRK2-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}