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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: 1-16986355-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=16986355&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 16986355,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_022089.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3409G>A",
"hgvs_p": "p.Val1137Met",
"transcript": "NM_022089.4",
"protein_id": "NP_071372.1",
"transcript_support_level": null,
"aa_start": 1137,
"aa_end": null,
"aa_length": 1180,
"cds_start": 3409,
"cds_end": null,
"cds_length": 3543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000326735.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022089.4"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3409G>A",
"hgvs_p": "p.Val1137Met",
"transcript": "ENST00000326735.13",
"protein_id": "ENSP00000327214.8",
"transcript_support_level": 1,
"aa_start": 1137,
"aa_end": null,
"aa_length": 1180,
"cds_start": 3409,
"cds_end": null,
"cds_length": 3543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_022089.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000326735.13"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3394G>A",
"hgvs_p": "p.Val1132Met",
"transcript": "ENST00000452699.5",
"protein_id": "ENSP00000413307.1",
"transcript_support_level": 1,
"aa_start": 1132,
"aa_end": null,
"aa_length": 1175,
"cds_start": 3394,
"cds_end": null,
"cds_length": 3528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000452699.5"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3107G>A",
"hgvs_p": "p.Arg1036His",
"transcript": "ENST00000341676.9",
"protein_id": "ENSP00000341115.5",
"transcript_support_level": 1,
"aa_start": 1036,
"aa_end": null,
"aa_length": 1158,
"cds_start": 3107,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000341676.9"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3394G>A",
"hgvs_p": "p.Val1132Met",
"transcript": "NM_001141973.3",
"protein_id": "NP_001135445.1",
"transcript_support_level": null,
"aa_start": 1132,
"aa_end": null,
"aa_length": 1175,
"cds_start": 3394,
"cds_end": null,
"cds_length": 3528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001141973.3"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3107G>A",
"hgvs_p": "p.Arg1036His",
"transcript": "NM_001141974.3",
"protein_id": "NP_001135446.1",
"transcript_support_level": null,
"aa_start": 1036,
"aa_end": null,
"aa_length": 1158,
"cds_start": 3107,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001141974.3"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.827G>A",
"hgvs_p": "p.Arg276His",
"transcript": "ENST00000502418.1",
"protein_id": "ENSP00000423065.1",
"transcript_support_level": 3,
"aa_start": 276,
"aa_end": null,
"aa_length": 398,
"cds_start": 827,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000502418.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3236G>A",
"hgvs_p": "p.Arg1079His",
"transcript": "XM_005245810.2",
"protein_id": "XP_005245867.1",
"transcript_support_level": null,
"aa_start": 1079,
"aa_end": null,
"aa_length": 1201,
"cds_start": 3236,
"cds_end": null,
"cds_length": 3606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005245810.2"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3224G>A",
"hgvs_p": "p.Arg1075His",
"transcript": "XM_005245811.2",
"protein_id": "XP_005245868.1",
"transcript_support_level": null,
"aa_start": 1075,
"aa_end": null,
"aa_length": 1197,
"cds_start": 3224,
"cds_end": null,
"cds_length": 3594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005245811.2"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3224G>A",
"hgvs_p": "p.Arg1075His",
"transcript": "XM_011541128.2",
"protein_id": "XP_011539430.1",
"transcript_support_level": null,
"aa_start": 1075,
"aa_end": null,
"aa_length": 1197,
"cds_start": 3224,
"cds_end": null,
"cds_length": 3594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541128.2"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3221G>A",
"hgvs_p": "p.Arg1074His",
"transcript": "XM_006710512.2",
"protein_id": "XP_006710575.1",
"transcript_support_level": null,
"aa_start": 1074,
"aa_end": null,
"aa_length": 1196,
"cds_start": 3221,
"cds_end": null,
"cds_length": 3591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006710512.2"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3221G>A",
"hgvs_p": "p.Arg1074His",
"transcript": "XM_047416537.1",
"protein_id": "XP_047272493.1",
"transcript_support_level": null,
"aa_start": 1074,
"aa_end": null,
"aa_length": 1196,
"cds_start": 3221,
"cds_end": null,
"cds_length": 3591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416537.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3212G>A",
"hgvs_p": "p.Arg1071His",
"transcript": "XM_005245812.2",
"protein_id": "XP_005245869.1",
"transcript_support_level": null,
"aa_start": 1071,
"aa_end": null,
"aa_length": 1193,
"cds_start": 3212,
"cds_end": null,
"cds_length": 3582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005245812.2"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3209G>A",
"hgvs_p": "p.Arg1070His",
"transcript": "XM_047416538.1",
"protein_id": "XP_047272494.1",
"transcript_support_level": null,
"aa_start": 1070,
"aa_end": null,
"aa_length": 1192,
"cds_start": 3209,
"cds_end": null,
"cds_length": 3579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416538.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3209G>A",
"hgvs_p": "p.Arg1070His",
"transcript": "XM_047416539.1",
"protein_id": "XP_047272495.1",
"transcript_support_level": null,
"aa_start": 1070,
"aa_end": null,
"aa_length": 1192,
"cds_start": 3209,
"cds_end": null,
"cds_length": 3579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416539.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3197G>A",
"hgvs_p": "p.Arg1066His",
"transcript": "XM_006710513.2",
"protein_id": "XP_006710576.1",
"transcript_support_level": null,
"aa_start": 1066,
"aa_end": null,
"aa_length": 1188,
"cds_start": 3197,
"cds_end": null,
"cds_length": 3567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006710513.2"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3194G>A",
"hgvs_p": "p.Arg1065His",
"transcript": "XM_047416542.1",
"protein_id": "XP_047272498.1",
"transcript_support_level": null,
"aa_start": 1065,
"aa_end": null,
"aa_length": 1187,
"cds_start": 3194,
"cds_end": null,
"cds_length": 3564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416542.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3406G>A",
"hgvs_p": "p.Val1136Met",
"transcript": "XM_047416544.1",
"protein_id": "XP_047272500.1",
"transcript_support_level": null,
"aa_start": 1136,
"aa_end": null,
"aa_length": 1179,
"cds_start": 3406,
"cds_end": null,
"cds_length": 3540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416544.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3394G>A",
"hgvs_p": "p.Val1132Met",
"transcript": "XM_017000844.2",
"protein_id": "XP_016856333.1",
"transcript_support_level": null,
"aa_start": 1132,
"aa_end": null,
"aa_length": 1175,
"cds_start": 3394,
"cds_end": null,
"cds_length": 3528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000844.2"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3391G>A",
"hgvs_p": "p.Val1131Met",
"transcript": "XM_017000845.2",
"protein_id": "XP_016856334.1",
"transcript_support_level": null,
"aa_start": 1131,
"aa_end": null,
"aa_length": 1174,
"cds_start": 3391,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000845.2"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3391G>A",
"hgvs_p": "p.Val1131Met",
"transcript": "XM_047416546.1",
"protein_id": "XP_047272502.1",
"transcript_support_level": null,
"aa_start": 1131,
"aa_end": null,
"aa_length": 1174,
"cds_start": 3391,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416546.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.3382G>A",
"hgvs_p": "p.Val1128Met",
"transcript": "XM_047416547.1",
"protein_id": "XP_047272503.1",
"transcript_support_level": null,
"aa_start": 1128,
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{
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{
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{
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],
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{
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],
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"biotype": "pseudogene",
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],
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"dbsnp": "rs528943677",
"frequency_reference_population": 0.000022792081,
"hom_count_reference_population": 0,
"allele_count_reference_population": 36,
"gnomad_exomes_af": 0.000016114,
"gnomad_genomes_af": 0.000085433,
"gnomad_exomes_ac": 23,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04685258865356445,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.226,
"revel_prediction": "Benign",
"alphamissense_score": 0.0739,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.133,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_022089.4",
"gene_symbol": "ATP13A2",
"hgnc_id": 30213,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3409G>A",
"hgvs_p": "p.Val1137Met"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000446261.1",
"gene_symbol": "ENSG00000226526",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.187+7243C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal recessive spastic paraplegia type 78,Inborn genetic diseases,Kufor-Rakeb syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Kufor-Rakeb syndrome;Autosomal recessive spastic paraplegia type 78|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}