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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: 3-139350279-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=139350279&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 139350279,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000680020.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.605G>A",
"hgvs_p": "p.Arg202His",
"transcript": "NM_020191.4",
"protein_id": "NP_064576.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 360,
"cds_start": 605,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 612,
"cdna_end": null,
"cdna_length": 1205,
"mane_select": "ENST00000680020.1",
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.605G>A",
"hgvs_p": "p.Arg202His",
"transcript": "ENST00000680020.1",
"protein_id": "ENSP00000505414.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 360,
"cds_start": 605,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 612,
"cdna_end": null,
"cdna_length": 1205,
"mane_select": "NM_020191.4",
"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": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.605G>A",
"hgvs_p": "p.Arg202His",
"transcript": "ENST00000495075.5",
"protein_id": "ENSP00000418008.1",
"transcript_support_level": 1,
"aa_start": 202,
"aa_end": null,
"aa_length": 360,
"cds_start": 605,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 1037,
"cdna_end": null,
"cdna_length": 1547,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.602G>A",
"hgvs_p": "p.Arg201His",
"transcript": "ENST00000310776.9",
"protein_id": "ENSP00000310785.5",
"transcript_support_level": 1,
"aa_start": 201,
"aa_end": null,
"aa_length": 359,
"cds_start": 602,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 609,
"cdna_end": null,
"cdna_length": 1202,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "n.619G>A",
"hgvs_p": null,
"transcript": "ENST00000492644.2",
"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": 5584,
"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": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "n.*202G>A",
"hgvs_p": null,
"transcript": "ENST00000498505.5",
"protein_id": "ENSP00000420482.1",
"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": 1401,
"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": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "n.*202G>A",
"hgvs_p": null,
"transcript": "ENST00000498505.5",
"protein_id": "ENSP00000420482.1",
"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": 1401,
"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": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.605G>A",
"hgvs_p": "p.Arg202His",
"transcript": "ENST00000688697.1",
"protein_id": "ENSP00000510396.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 360,
"cds_start": 605,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 1164,
"cdna_end": null,
"cdna_length": 5125,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.602G>A",
"hgvs_p": "p.Arg201His",
"transcript": "NM_001363893.1",
"protein_id": "NP_001350822.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 359,
"cds_start": 602,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 635,
"cdna_end": null,
"cdna_length": 1239,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.605G>A",
"hgvs_p": "p.Arg202His",
"transcript": "ENST00000686433.1",
"protein_id": "ENSP00000509173.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 342,
"cds_start": 605,
"cds_end": null,
"cds_length": 1029,
"cdna_start": 618,
"cdna_end": null,
"cdna_length": 3289,
"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": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.605G>A",
"hgvs_p": "p.Arg202His",
"transcript": "ENST00000691070.1",
"protein_id": "ENSP00000509723.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 332,
"cds_start": 605,
"cds_end": null,
"cds_length": 999,
"cdna_start": 605,
"cdna_end": null,
"cdna_length": 3246,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.605G>A",
"hgvs_p": "p.Arg202His",
"transcript": "ENST00000480644.2",
"protein_id": "ENSP00000420229.2",
"transcript_support_level": 3,
"aa_start": 202,
"aa_end": null,
"aa_length": 329,
"cds_start": 605,
"cds_end": null,
"cds_length": 990,
"cdna_start": 612,
"cdna_end": null,
"cdna_length": 1864,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.482G>A",
"hgvs_p": "p.Arg161His",
"transcript": "NM_001363857.1",
"protein_id": "NP_001350786.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 319,
"cds_start": 482,
"cds_end": null,
"cds_length": 960,
"cdna_start": 601,
"cdna_end": null,
"cdna_length": 1205,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.395G>A",
"hgvs_p": "p.Arg132His",
"transcript": "ENST00000478464.6",
"protein_id": "ENSP00000419303.2",
"transcript_support_level": 5,
"aa_start": 132,
"aa_end": null,
"aa_length": 290,
"cds_start": 395,
"cds_end": null,
"cds_length": 873,
"cdna_start": 587,
"cdna_end": null,
"cdna_length": 4352,
"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": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.395G>A",
"hgvs_p": "p.Arg132His",
"transcript": "ENST00000687538.1",
"protein_id": "ENSP00000508887.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 290,
"cds_start": 395,
"cds_end": null,
"cds_length": 873,
"cdna_start": 1029,
"cdna_end": null,
"cdna_length": 4794,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.395G>A",
"hgvs_p": "p.Arg132His",
"transcript": "ENST00000689286.1",
"protein_id": "ENSP00000509897.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 290,
"cds_start": 395,
"cds_end": null,
"cds_length": 873,
"cdna_start": 912,
"cdna_end": null,
"cdna_length": 4677,
"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": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "c.224G>A",
"hgvs_p": "p.Arg75His",
"transcript": "ENST00000684961.1",
"protein_id": "ENSP00000508439.1",
"transcript_support_level": null,
"aa_start": 75,
"aa_end": null,
"aa_length": 233,
"cds_start": 224,
"cds_end": null,
"cds_length": 702,
"cdna_start": 573,
"cdna_end": null,
"cdna_length": 4338,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "n.*202G>A",
"hgvs_p": null,
"transcript": "ENST00000466690.5",
"protein_id": "ENSP00000419737.1",
"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": 827,
"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": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "n.605G>A",
"hgvs_p": null,
"transcript": "ENST00000480938.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 1774,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "n.345G>A",
"hgvs_p": null,
"transcript": "ENST00000483545.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 568,
"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": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "n.*246G>A",
"hgvs_p": null,
"transcript": "ENST00000690298.1",
"protein_id": "ENSP00000509376.1",
"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": 4211,
"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": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "n.2473G>A",
"hgvs_p": null,
"transcript": "ENST00000692727.1",
"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": 6557,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS22",
"gene_hgnc_id": 14508,
"hgvs_c": "n.628G>A",
"hgvs_p": null,
"transcript": "ENST00000693155.1",
"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,
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},
{
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},
{
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"intron_variant"
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},
{
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"downstream_gene_variant"
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"gene_symbol": "MRPS22",
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}
],
"gene_symbol": "MRPS22",
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"dbsnp": "rs753345594",
"frequency_reference_population": 0.000016109087,
"hom_count_reference_population": 0,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.0000157336,
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"gnomad_genomes_ac": 3,
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"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9897733926773071,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.854,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5226,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.44,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.125,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000680020.1",
"gene_symbol": "MRPS22",
"hgnc_id": 14508,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.605G>A",
"hgvs_p": "p.Arg202His"
}
],
"clinvar_disease": " adult-onset, with leukoencephalopathy,46 XX gonadal dysgenesis,Muscular dystrophy,Ovarian dysgenesis 7,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 US:2",
"phenotype_combined": "46 XX gonadal dysgenesis|not provided|Ovarian dysgenesis 7|Muscular dystrophy, adult-onset, with leukoencephalopathy",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}