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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: 9-131518945-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=131518945&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 131518945,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000402686.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1474C>T",
"hgvs_p": "p.Arg492*",
"transcript": "NM_001077365.2",
"protein_id": "NP_001070833.1",
"transcript_support_level": null,
"aa_start": 492,
"aa_end": null,
"aa_length": 725,
"cds_start": 1474,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 1660,
"cdna_end": null,
"cdna_length": 3057,
"mane_select": "ENST00000402686.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1474C>T",
"hgvs_p": "p.Arg492*",
"transcript": "ENST00000402686.8",
"protein_id": "ENSP00000385797.4",
"transcript_support_level": 1,
"aa_start": 492,
"aa_end": null,
"aa_length": 725,
"cds_start": 1474,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 1660,
"cdna_end": null,
"cdna_length": 3057,
"mane_select": "NM_001077365.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*",
"transcript": "ENST00000372228.9",
"protein_id": "ENSP00000361302.3",
"transcript_support_level": 1,
"aa_start": 514,
"aa_end": null,
"aa_length": 747,
"cds_start": 1540,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 1855,
"cdna_end": null,
"cdna_length": 3252,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1531C>T",
"hgvs_p": "p.Arg511*",
"transcript": "ENST00000423007.6",
"protein_id": "ENSP00000404119.2",
"transcript_support_level": 1,
"aa_start": 511,
"aa_end": null,
"aa_length": 744,
"cds_start": 1531,
"cds_end": null,
"cds_length": 2235,
"cdna_start": 1531,
"cdna_end": null,
"cdna_length": 2235,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*",
"transcript": "NM_001353193.2",
"protein_id": "NP_001340122.2",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 747,
"cds_start": 1540,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 1966,
"cdna_end": null,
"cdna_length": 3363,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*",
"transcript": "NM_007171.4",
"protein_id": "NP_009102.4",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 747,
"cds_start": 1540,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 1726,
"cdna_end": null,
"cdna_length": 3123,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1474C>T",
"hgvs_p": "p.Arg492*",
"transcript": "NM_001136113.2",
"protein_id": "NP_001129585.1",
"transcript_support_level": null,
"aa_start": 492,
"aa_end": null,
"aa_length": 725,
"cds_start": 1474,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 1900,
"cdna_end": null,
"cdna_length": 3297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1474C>T",
"hgvs_p": "p.Arg492*",
"transcript": "ENST00000676640.1",
"protein_id": "ENSP00000503281.1",
"transcript_support_level": null,
"aa_start": 492,
"aa_end": null,
"aa_length": 725,
"cds_start": 1474,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 1912,
"cdna_end": null,
"cdna_length": 3309,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1462C>T",
"hgvs_p": "p.Arg488*",
"transcript": "NM_001374689.1",
"protein_id": "NP_001361618.1",
"transcript_support_level": null,
"aa_start": 488,
"aa_end": null,
"aa_length": 721,
"cds_start": 1462,
"cds_end": null,
"cds_length": 2166,
"cdna_start": 1658,
"cdna_end": null,
"cdna_length": 3055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1384C>T",
"hgvs_p": "p.Arg462*",
"transcript": "NM_001353196.2",
"protein_id": "NP_001340125.1",
"transcript_support_level": null,
"aa_start": 462,
"aa_end": null,
"aa_length": 695,
"cds_start": 1384,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 1570,
"cdna_end": null,
"cdna_length": 2967,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1384C>T",
"hgvs_p": "p.Arg462*",
"transcript": "ENST00000678303.1",
"protein_id": "ENSP00000503696.1",
"transcript_support_level": null,
"aa_start": 462,
"aa_end": null,
"aa_length": 695,
"cds_start": 1384,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 1540,
"cdna_end": null,
"cdna_length": 2573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1378C>T",
"hgvs_p": "p.Arg460*",
"transcript": "NM_001353197.2",
"protein_id": "NP_001340126.2",
"transcript_support_level": null,
"aa_start": 460,
"aa_end": null,
"aa_length": 693,
"cds_start": 1378,
"cds_end": null,
"cds_length": 2082,
"cdna_start": 1574,
"cdna_end": null,
"cdna_length": 2971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1378C>T",
"hgvs_p": "p.Arg460*",
"transcript": "NM_001353198.2",
"protein_id": "NP_001340127.2",
"transcript_support_level": null,
"aa_start": 460,
"aa_end": null,
"aa_length": 693,
"cds_start": 1378,
"cds_end": null,
"cds_length": 2082,
"cdna_start": 2275,
"cdna_end": null,
"cdna_length": 3672,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1312C>T",
"hgvs_p": "p.Arg438*",
"transcript": "NM_001077366.2",
"protein_id": "NP_001070834.1",
"transcript_support_level": null,
"aa_start": 438,
"aa_end": null,
"aa_length": 671,
"cds_start": 1312,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 1508,
"cdna_end": null,
"cdna_length": 2905,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1312C>T",
"hgvs_p": "p.Arg438*",
"transcript": "NM_001353194.2",
"protein_id": "NP_001340123.1",
"transcript_support_level": null,
"aa_start": 438,
"aa_end": null,
"aa_length": 671,
"cds_start": 1312,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 1748,
"cdna_end": null,
"cdna_length": 3145,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1312C>T",
"hgvs_p": "p.Arg438*",
"transcript": "ENST00000341012.13",
"protein_id": "ENSP00000343034.7",
"transcript_support_level": 2,
"aa_start": 438,
"aa_end": null,
"aa_length": 671,
"cds_start": 1312,
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"cds_length": 2016,
"cdna_start": 1531,
"cdna_end": null,
"cdna_length": 2935,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1189C>T",
"hgvs_p": "p.Arg397*",
"transcript": "NM_001353199.2",
"protein_id": "NP_001340128.2",
"transcript_support_level": null,
"aa_start": 397,
"aa_end": null,
"aa_length": 630,
"cds_start": 1189,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1467,
"cdna_end": null,
"cdna_length": 2864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1123C>T",
"hgvs_p": "p.Arg375*",
"transcript": "NM_001136114.2",
"protein_id": "NP_001129586.1",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 608,
"cds_start": 1123,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1401,
"cdna_end": null,
"cdna_length": 2798,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1123C>T",
"hgvs_p": "p.Arg375*",
"transcript": "NM_001353195.2",
"protein_id": "NP_001340124.1",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 608,
"cds_start": 1123,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1553,
"cdna_end": null,
"cdna_length": 2950,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1123C>T",
"hgvs_p": "p.Arg375*",
"transcript": "NM_001374691.1",
"protein_id": "NP_001361620.1",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 608,
"cds_start": 1123,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1590,
"cdna_end": null,
"cdna_length": 2987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1123C>T",
"hgvs_p": "p.Arg375*",
"transcript": "NM_001374692.1",
"protein_id": "NP_001361621.1",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 608,
"cds_start": 1123,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1502,
"cdna_end": null,
"cdna_length": 2899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1123C>T",
"hgvs_p": "p.Arg375*",
"transcript": "NM_001374693.1",
"protein_id": "NP_001361622.1",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 608,
"cds_start": 1123,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1319,
"cdna_end": null,
"cdna_length": 2716,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1123C>T",
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"computational_score_selected": 0.5299999713897705,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"alphamissense_score": null,
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"bayesdelnoaf_score": 0.53,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.724,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.11,
"spliceai_max_prediction": "Benign",
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"apogee2_score": null,
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"mitotip_score": null,
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"acmg_score": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000402686.8",
"gene_symbol": "POMT1",
"hgnc_id": 9202,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1474C>T",
"hgvs_p": "p.Arg492*"
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{
"score": 14,
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"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000415423.1",
"gene_symbol": "ENSG00000230289",
"hgnc_id": null,
"effects": [
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],
"inheritance_mode": "",
"hgvs_c": "n.63-1977G>A",
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}
],
"clinvar_disease": " type A1, type B1,Autosomal recessive limb-girdle muscular dystrophy type 2K,Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies),Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability),Walker-Warburg congenital muscular dystrophy,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4",
"phenotype_combined": "not provided|Walker-Warburg congenital muscular dystrophy;Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1;Autosomal recessive limb-girdle muscular dystrophy type 2K|Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1|Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1;Autosomal recessive limb-girdle muscular dystrophy type 2K;Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}