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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: 1-17000309-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=17000309&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 14,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ATP13A2",
"hgnc_id": 30213,
"hgvs_c": "c.844A>T",
"hgvs_p": "p.Ser282Cys",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -14,
"transcript": "NM_022089.4",
"verdict": "Benign"
},
{
"benign_score": 14,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000226526",
"hgnc_id": null,
"hgvs_c": "n.188-4334T>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -14,
"transcript": "ENST00000446261.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BS2",
"acmg_score": -14,
"allele_count_reference_population": 338,
"alphamissense_prediction": null,
"alphamissense_score": 0.1448,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.2,
"chr": "1",
"clinvar_classification": "Likely benign",
"clinvar_disease": "Autosomal recessive spastic paraplegia type 78,Kufor-Rakeb syndrome,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.07707607746124268,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1180,
"aa_ref": "S",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3996,
"cdna_start": 1034,
"cds_end": null,
"cds_length": 3543,
"cds_start": 844,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_022089.4",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.844A>T",
"hgvs_p": "p.Ser282Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000326735.13",
"protein_coding": true,
"protein_id": "NP_071372.1",
"strand": false,
"transcript": "NM_022089.4",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1180,
"aa_ref": "S",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3996,
"cdna_start": 1034,
"cds_end": null,
"cds_length": 3543,
"cds_start": 844,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000326735.13",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.844A>T",
"hgvs_p": "p.Ser282Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_022089.4",
"protein_coding": true,
"protein_id": "ENSP00000327214.8",
"strand": false,
"transcript": "ENST00000326735.13",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1175,
"aa_ref": "S",
"aa_start": 277,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3981,
"cdna_start": 1019,
"cds_end": null,
"cds_length": 3528,
"cds_start": 829,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000452699.5",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.829A>T",
"hgvs_p": "p.Ser277Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000413307.1",
"strand": false,
"transcript": "ENST00000452699.5",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1158,
"aa_ref": "S",
"aa_start": 277,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3681,
"cdna_start": 1006,
"cds_end": null,
"cds_length": 3477,
"cds_start": 829,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000341676.9",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.829A>T",
"hgvs_p": "p.Ser277Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000341115.5",
"strand": false,
"transcript": "ENST00000341676.9",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1175,
"aa_ref": "S",
"aa_start": 277,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3981,
"cdna_start": 1019,
"cds_end": null,
"cds_length": 3528,
"cds_start": 829,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001141973.3",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.829A>T",
"hgvs_p": "p.Ser277Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001135445.1",
"strand": false,
"transcript": "NM_001141973.3",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1158,
"aa_ref": "S",
"aa_start": 277,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3694,
"cdna_start": 1019,
"cds_end": null,
"cds_length": 3477,
"cds_start": 829,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001141974.3",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.829A>T",
"hgvs_p": "p.Ser277Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001135446.1",
"strand": false,
"transcript": "NM_001141974.3",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 319,
"aa_ref": "S",
"aa_start": 256,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 962,
"cdna_start": 767,
"cds_end": null,
"cds_length": 961,
"cds_start": 766,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000510069.5",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.766A>T",
"hgvs_p": "p.Ser256Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000424313.1",
"strand": false,
"transcript": "ENST00000510069.5",
"transcript_support_level": 5
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 190,
"aa_ref": "S",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 573,
"cdna_start": 4,
"cds_end": null,
"cds_length": 573,
"cds_start": 4,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000506174.5",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.4A>T",
"hgvs_p": "p.Ser2Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000424393.1",
"strand": false,
"transcript": "ENST00000506174.5",
"transcript_support_level": 5
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 188,
"aa_ref": "S",
"aa_start": 177,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 569,
"cdna_start": 529,
"cds_end": null,
"cds_length": 569,
"cds_start": 529,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000511957.5",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.529A>T",
"hgvs_p": "p.Ser177Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000427241.1",
"strand": false,
"transcript": "ENST00000511957.5",
"transcript_support_level": 5
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 186,
"aa_ref": "S",
"aa_start": 179,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 562,
"cdna_start": 536,
"cds_end": null,
"cds_length": 561,
"cds_start": 535,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000508222.5",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.535A>T",
"hgvs_p": "p.Ser179Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000422227.1",
"strand": false,
"transcript": "ENST00000508222.5",
"transcript_support_level": 4
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1201,
"aa_ref": "S",
"aa_start": 281,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3823,
"cdna_start": 1031,
"cds_end": null,
"cds_length": 3606,
"cds_start": 841,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_005245810.2",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.841A>T",
"hgvs_p": "p.Ser281Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005245867.1",
"strand": false,
"transcript": "XM_005245810.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1197,
"aa_ref": "S",
"aa_start": 277,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3811,
"cdna_start": 1019,
"cds_end": null,
"cds_length": 3594,
"cds_start": 829,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_005245811.2",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.829A>T",
"hgvs_p": "p.Ser277Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005245868.1",
"strand": false,
"transcript": "XM_005245811.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1197,
"aa_ref": "S",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3811,
"cdna_start": 1034,
"cds_end": null,
"cds_length": 3594,
"cds_start": 844,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011541128.2",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.844A>T",
"hgvs_p": "p.Ser282Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011539430.1",
"strand": false,
"transcript": "XM_011541128.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1196,
"aa_ref": "S",
"aa_start": 276,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3808,
"cdna_start": 1016,
"cds_end": null,
"cds_length": 3591,
"cds_start": 826,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_006710512.2",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.826A>T",
"hgvs_p": "p.Ser276Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006710575.1",
"strand": false,
"transcript": "XM_006710512.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1196,
"aa_ref": "S",
"aa_start": 281,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3808,
"cdna_start": 1031,
"cds_end": null,
"cds_length": 3591,
"cds_start": 841,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047416537.1",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.841A>T",
"hgvs_p": "p.Ser281Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272493.1",
"strand": false,
"transcript": "XM_047416537.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1193,
"aa_ref": "S",
"aa_start": 273,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3799,
"cdna_start": 1007,
"cds_end": null,
"cds_length": 3582,
"cds_start": 817,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_005245812.2",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.817A>T",
"hgvs_p": "p.Ser273Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005245869.1",
"strand": false,
"transcript": "XM_005245812.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
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"aa_length": 1192,
"aa_ref": "S",
"aa_start": 277,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3796,
"cdna_start": 1019,
"cds_end": null,
"cds_length": 3579,
"cds_start": 829,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047416538.1",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.829A>T",
"hgvs_p": "p.Ser277Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272494.1",
"strand": false,
"transcript": "XM_047416538.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1192,
"aa_ref": "S",
"aa_start": 272,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3796,
"cdna_start": 1004,
"cds_end": null,
"cds_length": 3579,
"cds_start": 814,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047416539.1",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.814A>T",
"hgvs_p": "p.Ser272Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272495.1",
"strand": false,
"transcript": "XM_047416539.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1188,
"aa_ref": "S",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3784,
"cdna_start": 992,
"cds_end": null,
"cds_length": 3567,
"cds_start": 802,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_006710513.2",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.802A>T",
"hgvs_p": "p.Ser268Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006710576.1",
"strand": false,
"transcript": "XM_006710513.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1187,
"aa_ref": "S",
"aa_start": 267,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3781,
"cdna_start": 989,
"cds_end": null,
"cds_length": 3564,
"cds_start": 799,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047416542.1",
"gene_hgnc_id": 30213,
"gene_symbol": "ATP13A2",
"hgvs_c": "c.799A>T",
"hgvs_p": "p.Ser267Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272498.1",
"strand": false,
"transcript": "XM_047416542.1",
"transcript_support_level": null
},
{
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