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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: 12-40335031-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=40335031&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 40335031,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000298910.12",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5822G>A",
"hgvs_p": "p.Arg1941His",
"transcript": "NM_198578.4",
"protein_id": "NP_940980.4",
"transcript_support_level": null,
"aa_start": 1941,
"aa_end": null,
"aa_length": 2527,
"cds_start": 5822,
"cds_end": null,
"cds_length": 7584,
"cdna_start": 5957,
"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"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5822G>A",
"hgvs_p": "p.Arg1941His",
"transcript": "ENST00000298910.12",
"protein_id": "ENSP00000298910.7",
"transcript_support_level": 1,
"aa_start": 1941,
"aa_end": null,
"aa_length": 2527,
"cds_start": 5822,
"cds_end": null,
"cds_length": 7584,
"cdna_start": 5957,
"cdna_end": null,
"cdna_length": 9239,
"mane_select": "NM_198578.4",
"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": 19,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*2495G>A",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6400,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*2495G>A",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6400,
"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"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5567G>A",
"hgvs_p": "p.Arg1856His",
"transcript": "ENST00000680790.1",
"protein_id": "ENSP00000505335.1",
"transcript_support_level": null,
"aa_start": 1856,
"aa_end": null,
"aa_length": 2442,
"cds_start": 5567,
"cds_end": null,
"cds_length": 7329,
"cdna_start": 5619,
"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"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.1505G>A",
"hgvs_p": "p.Arg502His",
"transcript": "ENST00000681696.1",
"protein_id": "ENSP00000505871.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 1052,
"cds_start": 1505,
"cds_end": null,
"cds_length": 3159,
"cdna_start": 1505,
"cdna_end": null,
"cdna_length": 3828,
"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"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5822G>A",
"hgvs_p": "p.Arg1941His",
"transcript": "XM_005268629.5",
"protein_id": "XP_005268686.1",
"transcript_support_level": null,
"aa_start": 1941,
"aa_end": null,
"aa_length": 2521,
"cds_start": 5822,
"cds_end": null,
"cds_length": 7566,
"cdna_start": 5957,
"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"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5822G>A",
"hgvs_p": "p.Arg1941His",
"transcript": "XM_011537877.4",
"protein_id": "XP_011536179.1",
"transcript_support_level": null,
"aa_start": 1941,
"aa_end": null,
"aa_length": 2503,
"cds_start": 5822,
"cds_end": null,
"cds_length": 7512,
"cdna_start": 5957,
"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"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5822G>A",
"hgvs_p": "p.Arg1941His",
"transcript": "XM_047428277.1",
"protein_id": "XP_047284233.1",
"transcript_support_level": null,
"aa_start": 1941,
"aa_end": null,
"aa_length": 2490,
"cds_start": 5822,
"cds_end": null,
"cds_length": 7473,
"cdna_start": 5957,
"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"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.5822G>A",
"hgvs_p": "p.Arg1941His",
"transcript": "XM_047428278.1",
"protein_id": "XP_047284234.1",
"transcript_support_level": null,
"aa_start": 1941,
"aa_end": null,
"aa_length": 2371,
"cds_start": 5822,
"cds_end": null,
"cds_length": 7116,
"cdna_start": 5957,
"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"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.4619G>A",
"hgvs_p": "p.Arg1540His",
"transcript": "XM_024448833.2",
"protein_id": "XP_024304601.1",
"transcript_support_level": null,
"aa_start": 1540,
"aa_end": null,
"aa_length": 2126,
"cds_start": 4619,
"cds_end": null,
"cds_length": 6381,
"cdna_start": 5121,
"cdna_end": null,
"cdna_length": 8403,
"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"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "c.2738G>A",
"hgvs_p": "p.Arg913His",
"transcript": "XM_017018787.2",
"protein_id": "XP_016874276.1",
"transcript_support_level": null,
"aa_start": 913,
"aa_end": null,
"aa_length": 1499,
"cds_start": 2738,
"cds_end": null,
"cds_length": 4500,
"cdna_start": 2887,
"cdna_end": null,
"cdna_length": 6169,
"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": 17,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.2503G>A",
"hgvs_p": null,
"transcript": "ENST00000479187.5",
"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": 8306,
"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": 41,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*4731G>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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*1082G>A",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4852,
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*1045G>A",
"hgvs_p": null,
"transcript": "ENST00000680018.1",
"protein_id": "ENSP00000505347.1",
"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": 4523,
"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": 10,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.1466G>A",
"hgvs_p": null,
"transcript": "ENST00000680422.1",
"protein_id": "ENSP00000505304.1",
"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": 8598,
"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": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*857G>A",
"hgvs_p": null,
"transcript": "ENST00000680425.1",
"protein_id": "ENSP00000506459.1",
"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": 3968,
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*798G>A",
"hgvs_p": null,
"transcript": "ENST00000680453.1",
"protein_id": "ENSP00000505566.1",
"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": 4515,
"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": 10,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.1806G>A",
"hgvs_p": null,
"transcript": "ENST00000681136.1",
"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": 4081,
"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": 40,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.5957G>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": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*4731G>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": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"hgvs_c": "n.*1082G>A",
"hgvs_p": null,
"transcript": "ENST00000679532.1",
"protein_id": "ENSP00000506435.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
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},
{
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},
{
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},
{
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},
{
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"consequences": [
"intron_variant"
],
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}
],
"gene_symbol": "LRRK2",
"gene_hgnc_id": 18618,
"dbsnp": "rs77428810",
"frequency_reference_population": 0.00020073653,
"hom_count_reference_population": 0,
"allele_count_reference_population": 324,
"gnomad_exomes_af": 0.00019838,
"gnomad_genomes_af": 0.000223367,
"gnomad_exomes_ac": 290,
"gnomad_genomes_ac": 34,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3281516432762146,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.24,
"revel_prediction": "Benign",
"alphamissense_score": 0.088,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.582,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000298910.12",
"gene_symbol": "LRRK2",
"hgnc_id": 18618,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.5822G>A",
"hgvs_p": "p.Arg1941His"
},
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "ENST00000724141.1",
"gene_symbol": "ENSG00000258167",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.308-12612C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal dominant Parkinson disease 8,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:6 O:1",
"phenotype_combined": "Autosomal dominant Parkinson disease 8|not specified|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}