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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: 5-119541982-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=119541982&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 119541982,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_000414.4",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.2199C>T",
"hgvs_p": "p.Tyr733Tyr",
"transcript": "NM_000414.4",
"protein_id": "NP_000405.1",
"transcript_support_level": null,
"aa_start": 733,
"aa_end": null,
"aa_length": 736,
"cds_start": 2199,
"cds_end": null,
"cds_length": 2211,
"cdna_start": 2278,
"cdna_end": null,
"cdna_length": 2628,
"mane_select": "ENST00000510025.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.2199C>T",
"hgvs_p": "p.Tyr733Tyr",
"transcript": "ENST00000510025.7",
"protein_id": "ENSP00000424940.3",
"transcript_support_level": 2,
"aa_start": 733,
"aa_end": null,
"aa_length": 736,
"cds_start": 2199,
"cds_end": null,
"cds_length": 2211,
"cdna_start": 2278,
"cdna_end": null,
"cdna_length": 2628,
"mane_select": "NM_000414.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.2130C>T",
"hgvs_p": "p.Tyr710Tyr",
"transcript": "ENST00000509514.6",
"protein_id": "ENSP00000426272.2",
"transcript_support_level": 1,
"aa_start": 710,
"aa_end": null,
"aa_length": 713,
"cds_start": 2130,
"cds_end": null,
"cds_length": 2142,
"cdna_start": 2230,
"cdna_end": null,
"cdna_length": 2566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.2274C>T",
"hgvs_p": "p.Tyr758Tyr",
"transcript": "NM_001199291.3",
"protein_id": "NP_001186220.1",
"transcript_support_level": null,
"aa_start": 758,
"aa_end": null,
"aa_length": 761,
"cds_start": 2274,
"cds_end": null,
"cds_length": 2286,
"cdna_start": 2531,
"cdna_end": null,
"cdna_length": 2881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.2274C>T",
"hgvs_p": "p.Tyr758Tyr",
"transcript": "ENST00000414835.7",
"protein_id": "ENSP00000411960.3",
"transcript_support_level": 2,
"aa_start": 758,
"aa_end": null,
"aa_length": 761,
"cds_start": 2274,
"cds_end": null,
"cds_length": 2286,
"cdna_start": 2531,
"cdna_end": null,
"cdna_length": 2881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.2190C>T",
"hgvs_p": "p.Tyr730Tyr",
"transcript": "NM_001374497.1",
"protein_id": "NP_001361426.1",
"transcript_support_level": null,
"aa_start": 730,
"aa_end": null,
"aa_length": 733,
"cds_start": 2190,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 2269,
"cdna_end": null,
"cdna_length": 2619,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.2145C>T",
"hgvs_p": "p.Tyr715Tyr",
"transcript": "NM_001199292.2",
"protein_id": "NP_001186221.1",
"transcript_support_level": null,
"aa_start": 715,
"aa_end": null,
"aa_length": 718,
"cds_start": 2145,
"cds_end": null,
"cds_length": 2157,
"cdna_start": 2224,
"cdna_end": null,
"cdna_length": 2574,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.2145C>T",
"hgvs_p": "p.Tyr715Tyr",
"transcript": "ENST00000515320.5",
"protein_id": "ENSP00000424613.1",
"transcript_support_level": 2,
"aa_start": 715,
"aa_end": null,
"aa_length": 718,
"cds_start": 2145,
"cds_end": null,
"cds_length": 2157,
"cdna_start": 2224,
"cdna_end": null,
"cdna_length": 2494,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.2127C>T",
"hgvs_p": "p.Tyr709Tyr",
"transcript": "NM_001292027.2",
"protein_id": "NP_001278956.1",
"transcript_support_level": null,
"aa_start": 709,
"aa_end": null,
"aa_length": 712,
"cds_start": 2127,
"cds_end": null,
"cds_length": 2139,
"cdna_start": 2343,
"cdna_end": null,
"cdna_length": 2693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.2127C>T",
"hgvs_p": "p.Tyr709Tyr",
"transcript": "NM_001374498.1",
"protein_id": "NP_001361427.1",
"transcript_support_level": null,
"aa_start": 709,
"aa_end": null,
"aa_length": 712,
"cds_start": 2127,
"cds_end": null,
"cds_length": 2139,
"cdna_start": 2206,
"cdna_end": null,
"cdna_length": 2556,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.2127C>T",
"hgvs_p": "p.Tyr709Tyr",
"transcript": "ENST00000682996.1",
"protein_id": "ENSP00000507792.1",
"transcript_support_level": null,
"aa_start": 709,
"aa_end": null,
"aa_length": 712,
"cds_start": 2127,
"cds_end": null,
"cds_length": 2139,
"cdna_start": 2227,
"cdna_end": null,
"cdna_length": 2563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.1872C>T",
"hgvs_p": "p.Tyr624Tyr",
"transcript": "NM_001374499.1",
"protein_id": "NP_001361428.1",
"transcript_support_level": null,
"aa_start": 624,
"aa_end": null,
"aa_length": 627,
"cds_start": 1872,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 2484,
"cdna_end": null,
"cdna_length": 2834,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.1788C>T",
"hgvs_p": "p.Tyr596Tyr",
"transcript": "NM_001374501.1",
"protein_id": "NP_001361430.1",
"transcript_support_level": null,
"aa_start": 596,
"aa_end": null,
"aa_length": 599,
"cds_start": 1788,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 2466,
"cdna_end": null,
"cdna_length": 2816,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.1788C>T",
"hgvs_p": "p.Tyr596Tyr",
"transcript": "NM_001374502.1",
"protein_id": "NP_001361431.1",
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"aa_start": 596,
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"cds_start": 1788,
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"cdna_start": 2471,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.1788C>T",
"hgvs_p": "p.Tyr596Tyr",
"transcript": "NM_001374503.1",
"protein_id": "NP_001361432.1",
"transcript_support_level": null,
"aa_start": 596,
"aa_end": null,
"aa_length": 599,
"cds_start": 1788,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 2536,
"cdna_end": null,
"cdna_length": 2886,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.1788C>T",
"hgvs_p": "p.Tyr596Tyr",
"transcript": "ENST00000513628.5",
"protein_id": "ENSP00000425993.1",
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"aa_start": 596,
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"cds_start": 1788,
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"cdna_start": 2033,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.1779C>T",
"hgvs_p": "p.Tyr593Tyr",
"transcript": "NM_001292028.2",
"protein_id": "NP_001278957.1",
"transcript_support_level": null,
"aa_start": 593,
"aa_end": null,
"aa_length": 596,
"cds_start": 1779,
"cds_end": null,
"cds_length": 1791,
"cdna_start": 2457,
"cdna_end": null,
"cdna_length": 2807,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.1758C>T",
"hgvs_p": "p.Tyr586Tyr",
"transcript": "NM_001374500.1",
"protein_id": "NP_001361429.1",
"transcript_support_level": null,
"aa_start": 586,
"aa_end": null,
"aa_length": 589,
"cds_start": 1758,
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"cds_length": 1770,
"cdna_start": 2563,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.1758C>T",
"hgvs_p": "p.Tyr586Tyr",
"transcript": "ENST00000645099.1",
"protein_id": "ENSP00000496091.1",
"transcript_support_level": null,
"aa_start": 586,
"aa_end": null,
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"cdna_start": 2093,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "c.1443C>T",
"hgvs_p": "p.Tyr481Tyr",
"transcript": "ENST00000518349.6",
"protein_id": "ENSP00000507185.1",
"transcript_support_level": 5,
"aa_start": 481,
"aa_end": null,
"aa_length": 484,
"cds_start": 1443,
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"cdna_start": 1498,
"cdna_end": null,
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"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "n.*754C>T",
"hgvs_p": null,
"transcript": "ENST00000442060.7",
"protein_id": "ENSP00000390208.3",
"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": 2686,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B4",
"gene_hgnc_id": 5213,
"hgvs_c": "n.859C>T",
"hgvs_p": null,
"transcript": "ENST00000503310.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 1129,
"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,
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"frequency_reference_population": 0.00987302,
"hom_count_reference_population": 711,
"allele_count_reference_population": 15888,
"gnomad_exomes_af": 0.00707842,
"gnomad_genomes_af": 0.0366397,
"gnomad_exomes_ac": 10314,
"gnomad_genomes_ac": 5574,
"gnomad_exomes_homalt": 415,
"gnomad_genomes_homalt": 296,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6800000071525574,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.68,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.408,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_000414.4",
"gene_symbol": "HSD17B4",
"hgnc_id": 5213,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2199C>T",
"hgvs_p": "p.Tyr733Tyr"
}
],
"clinvar_disease": "Bifunctional peroxisomal enzyme deficiency,Perrault syndrome,Perrault syndrome 1,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:7",
"phenotype_combined": "not specified|Perrault syndrome;Bifunctional peroxisomal enzyme deficiency|Perrault syndrome 1|Bifunctional peroxisomal enzyme deficiency|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}