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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: 1-43920835-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=43920835&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 43920835,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000347631.8",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "c.945C>T",
"hgvs_p": "p.Asp315Asp",
"transcript": "NM_006279.5",
"protein_id": "NP_006270.1",
"transcript_support_level": null,
"aa_start": 315,
"aa_end": null,
"aa_length": 375,
"cds_start": 945,
"cds_end": null,
"cds_length": 1128,
"cdna_start": 1133,
"cdna_end": null,
"cdna_length": 2254,
"mane_select": "ENST00000347631.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "c.945C>T",
"hgvs_p": "p.Asp315Asp",
"transcript": "ENST00000347631.8",
"protein_id": "ENSP00000317192.6",
"transcript_support_level": 5,
"aa_start": 315,
"aa_end": null,
"aa_length": 375,
"cds_start": 945,
"cds_end": null,
"cds_length": 1128,
"cdna_start": 1133,
"cdna_end": null,
"cdna_length": 2254,
"mane_select": "NM_006279.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "c.1059C>T",
"hgvs_p": "p.Asp353Asp",
"transcript": "ENST00000372372.7",
"protein_id": "ENSP00000361447.2",
"transcript_support_level": 1,
"aa_start": 353,
"aa_end": null,
"aa_length": 413,
"cds_start": 1059,
"cds_end": null,
"cds_length": 1242,
"cdna_start": 1256,
"cdna_end": null,
"cdna_length": 2109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "c.1038C>T",
"hgvs_p": "p.Asp346Asp",
"transcript": "ENST00000361746.9",
"protein_id": "ENSP00000354657.5",
"transcript_support_level": 1,
"aa_start": 346,
"aa_end": null,
"aa_length": 406,
"cds_start": 1038,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 1115,
"cdna_end": null,
"cdna_length": 2229,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "c.990C>T",
"hgvs_p": "p.Asp330Asp",
"transcript": "ENST00000361392.9",
"protein_id": "ENSP00000355341.5",
"transcript_support_level": 1,
"aa_start": 330,
"aa_end": null,
"aa_length": 390,
"cds_start": 990,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 1176,
"cdna_end": null,
"cdna_length": 2297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "c.897C>T",
"hgvs_p": "p.Asp299Asp",
"transcript": "ENST00000361400.9",
"protein_id": "ENSP00000354748.4",
"transcript_support_level": 1,
"aa_start": 299,
"aa_end": null,
"aa_length": 359,
"cds_start": 897,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 1088,
"cdna_end": null,
"cdna_length": 2212,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "c.855C>T",
"hgvs_p": "p.Asp285Asp",
"transcript": "ENST00000372369.5",
"protein_id": "ENSP00000361444.1",
"transcript_support_level": 1,
"aa_start": 285,
"aa_end": null,
"aa_length": 345,
"cds_start": 855,
"cds_end": null,
"cds_length": 1038,
"cdna_start": 855,
"cdna_end": null,
"cdna_length": 1038,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "c.729C>T",
"hgvs_p": "p.Asp243Asp",
"transcript": "ENST00000332628.11",
"protein_id": "ENSP00000329755.7",
"transcript_support_level": 1,
"aa_start": 243,
"aa_end": null,
"aa_length": 303,
"cds_start": 729,
"cds_end": null,
"cds_length": 912,
"cdna_start": 731,
"cdna_end": null,
"cdna_length": 1681,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "n.*571C>T",
"hgvs_p": null,
"transcript": "ENST00000469715.6",
"protein_id": "ENSP00000431700.2",
"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": 1277,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "n.*722C>T",
"hgvs_p": null,
"transcript": "ENST00000490541.6",
"protein_id": "ENSP00000435018.2",
"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": 1037,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "n.*23C>T",
"hgvs_p": null,
"transcript": "ENST00000530581.5",
"protein_id": "ENSP00000437293.1",
"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": 893,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "n.*142C>T",
"hgvs_p": null,
"transcript": "ENST00000533212.5",
"protein_id": "ENSP00000435621.1",
"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": 781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000284989",
"gene_hgnc_id": null,
"hgvs_c": "n.*2267C>T",
"hgvs_p": null,
"transcript": "ENST00000645057.1",
"protein_id": "ENSP00000494063.1",
"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": 4037,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "n.*571C>T",
"hgvs_p": null,
"transcript": "ENST00000469715.6",
"protein_id": "ENSP00000431700.2",
"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,
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"cdna_length": 1277,
"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": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "n.*722C>T",
"hgvs_p": null,
"transcript": "ENST00000490541.6",
"protein_id": "ENSP00000435018.2",
"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": 1037,
"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": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "n.*23C>T",
"hgvs_p": null,
"transcript": "ENST00000530581.5",
"protein_id": "ENSP00000437293.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 893,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "n.*142C>T",
"hgvs_p": null,
"transcript": "ENST00000533212.5",
"protein_id": "ENSP00000435621.1",
"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": 781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000284989",
"gene_hgnc_id": null,
"hgvs_c": "n.*2267C>T",
"hgvs_p": null,
"transcript": "ENST00000645057.1",
"protein_id": "ENSP00000494063.1",
"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": 4037,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "c.1053+285C>T",
"hgvs_p": null,
"transcript": "ENST00000372368.7",
"protein_id": "ENSP00000361443.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 380,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "c.834+285C>T",
"hgvs_p": null,
"transcript": "ENST00000533933.6",
"protein_id": "ENSP00000432965.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 307,
"cds_start": -4,
"cds_end": null,
"cds_length": 924,
"cdna_start": null,
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"cdna_length": 1844,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "c.604-9297C>T",
"hgvs_p": null,
"transcript": "ENST00000531993.6",
"protein_id": "ENSP00000432682.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 230,
"cds_start": -4,
"cds_end": null,
"cds_length": 693,
"cdna_start": null,
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"cdna_length": 693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "c.555-9297C>T",
"hgvs_p": null,
"transcript": "ENST00000372367.5",
"protein_id": "ENSP00000361442.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 201,
"cds_start": -4,
"cds_end": null,
"cds_length": 606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "ST3GAL3",
"gene_hgnc_id": 10866,
"hgvs_c": "c.*23-9297C>T",
"hgvs_p": null,
"transcript": "ENST00000372365.5",
"protein_id": "ENSP00000361440.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
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"gnomad_exomes_af": 0.0000253097,
"gnomad_genomes_af": 0.0000460163,
"gnomad_exomes_ac": 37,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2800000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.28,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.3,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.155,
"phylop100way_prediction": "Benign",
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4,BP6,BP7,BS1",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000347631.8",
"gene_symbol": "ST3GAL3",
"hgnc_id": 10866,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.945C>T",
"hgvs_p": "p.Asp315Asp"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000645057.1",
"gene_symbol": "ENSG00000284989",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*2267C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Developmental and epileptic encephalopathy,Inborn genetic diseases,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:2",
"phenotype_combined": "not specified|Developmental and epileptic encephalopathy|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}