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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: 1-16997013-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=16997013&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 16997013,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000326735.13",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1195+7G>A",
"hgvs_p": null,
"transcript": "NM_022089.4",
"protein_id": "NP_071372.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1180,
"cds_start": -4,
"cds_end": null,
"cds_length": 3543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3996,
"mane_select": "ENST00000326735.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1195+7G>A",
"hgvs_p": null,
"transcript": "ENST00000326735.13",
"protein_id": "ENSP00000327214.8",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1180,
"cds_start": -4,
"cds_end": null,
"cds_length": 3543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3996,
"mane_select": "NM_022089.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1180+7G>A",
"hgvs_p": null,
"transcript": "ENST00000452699.5",
"protein_id": "ENSP00000413307.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1175,
"cds_start": -4,
"cds_end": null,
"cds_length": 3528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1180+7G>A",
"hgvs_p": null,
"transcript": "ENST00000341676.9",
"protein_id": "ENSP00000341115.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1158,
"cds_start": -4,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "n.334+7G>A",
"hgvs_p": null,
"transcript": "ENST00000502860.1",
"protein_id": null,
"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": 687,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1180+7G>A",
"hgvs_p": null,
"transcript": "NM_001141973.3",
"protein_id": "NP_001135445.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1175,
"cds_start": -4,
"cds_end": null,
"cds_length": 3528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1180+7G>A",
"hgvs_p": null,
"transcript": "NM_001141974.3",
"protein_id": "NP_001135446.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1158,
"cds_start": -4,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3694,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.355+7G>A",
"hgvs_p": null,
"transcript": "ENST00000506174.5",
"protein_id": "ENSP00000424393.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 190,
"cds_start": -4,
"cds_end": null,
"cds_length": 573,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000226526",
"gene_hgnc_id": null,
"hgvs_c": "n.188-7630C>T",
"hgvs_p": null,
"transcript": "ENST00000446261.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "n.803+7G>A",
"hgvs_p": null,
"transcript": "ENST00000463860.5",
"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": 1639,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1192+7G>A",
"hgvs_p": null,
"transcript": "XM_005245810.2",
"protein_id": "XP_005245867.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1201,
"cds_start": -4,
"cds_end": null,
"cds_length": 3606,
"cdna_start": null,
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"cdna_length": 3823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1180+7G>A",
"hgvs_p": null,
"transcript": "XM_005245811.2",
"protein_id": "XP_005245868.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1197,
"cds_start": -4,
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"cds_length": 3594,
"cdna_start": null,
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"cdna_length": 3811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1195+7G>A",
"hgvs_p": null,
"transcript": "XM_011541128.2",
"protein_id": "XP_011539430.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 1197,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1177+7G>A",
"hgvs_p": null,
"transcript": "XM_006710512.2",
"protein_id": "XP_006710575.1",
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"aa_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1192+7G>A",
"hgvs_p": null,
"transcript": "XM_047416537.1",
"protein_id": "XP_047272493.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1196,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1168+7G>A",
"hgvs_p": null,
"transcript": "XM_005245812.2",
"protein_id": "XP_005245869.1",
"transcript_support_level": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1180+7G>A",
"hgvs_p": null,
"transcript": "XM_047416538.1",
"protein_id": "XP_047272494.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1192,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 3796,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1165+7G>A",
"hgvs_p": null,
"transcript": "XM_047416539.1",
"protein_id": "XP_047272495.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 1192,
"cds_start": -4,
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"cdna_start": null,
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},
{
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"canonical": false,
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"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
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"exon_count": 28,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1153+7G>A",
"hgvs_p": null,
"transcript": "XM_006710513.2",
"protein_id": "XP_006710576.1",
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1150+7G>A",
"hgvs_p": null,
"transcript": "XM_047416542.1",
"protein_id": "XP_047272498.1",
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},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
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"exon_count": 29,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1192+7G>A",
"hgvs_p": null,
"transcript": "XM_047416544.1",
"protein_id": "XP_047272500.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1179,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 3993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.1195+7G>A",
"hgvs_p": null,
"transcript": "XM_017000844.2",
"protein_id": "XP_016856333.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1175,
"cds_start": -4,
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"cds_length": 3528,
"cdna_start": null,
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"cdna_length": 3981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
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}
],
"gene_symbol": "ATP13A2",
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"gnomad_exomes_homalt": 0,
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"computational_score_selected": -0.8600000143051147,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
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"revel_prediction": null,
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"bayesdelnoaf_score": -0.86,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.013,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000235096111034878,
"dbscsnv_ada_prediction": "Benign",
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"mitotip_score": null,
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"acmg_score": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000326735.13",
"gene_symbol": "ATP13A2",
"hgnc_id": 30213,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1195+7G>A",
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},
{
"score": -4,
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"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000446261.1",
"gene_symbol": "ENSG00000226526",
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"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.188-7630C>T",
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}
],
"clinvar_disease": "Autosomal recessive spastic paraplegia type 78,Kufor-Rakeb syndrome",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Autosomal recessive spastic paraplegia type 78;Kufor-Rakeb syndrome",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}