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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: 2-47806624-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=47806624&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 47806624,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000179.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3974A>C",
"hgvs_p": "p.Lys1325Thr",
"transcript": "NM_000179.3",
"protein_id": "NP_000170.1",
"transcript_support_level": null,
"aa_start": 1325,
"aa_end": null,
"aa_length": 1360,
"cds_start": 3974,
"cds_end": null,
"cds_length": 4083,
"cdna_start": 4063,
"cdna_end": null,
"cdna_length": 4265,
"mane_select": "ENST00000234420.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3974A>C",
"hgvs_p": "p.Lys1325Thr",
"transcript": "ENST00000234420.11",
"protein_id": "ENSP00000234420.5",
"transcript_support_level": 1,
"aa_start": 1325,
"aa_end": null,
"aa_length": 1360,
"cds_start": 3974,
"cds_end": null,
"cds_length": 4083,
"cdna_start": 4063,
"cdna_end": null,
"cdna_length": 4265,
"mane_select": "NM_000179.3",
"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": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "n.*3321A>C",
"hgvs_p": null,
"transcript": "ENST00000445503.5",
"protein_id": "ENSP00000405294.1",
"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": 4158,
"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": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "n.*3321A>C",
"hgvs_p": null,
"transcript": "ENST00000445503.5",
"protein_id": "ENSP00000405294.1",
"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": 4158,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.4070A>C",
"hgvs_p": "p.Lys1357Thr",
"transcript": "NM_001406795.1",
"protein_id": "NP_001393724.1",
"transcript_support_level": null,
"aa_start": 1357,
"aa_end": null,
"aa_length": 1392,
"cds_start": 4070,
"cds_end": null,
"cds_length": 4179,
"cdna_start": 4159,
"cdna_end": null,
"cdna_length": 4361,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3980A>C",
"hgvs_p": "p.Lys1327Thr",
"transcript": "NM_001406813.1",
"protein_id": "NP_001393742.1",
"transcript_support_level": null,
"aa_start": 1327,
"aa_end": null,
"aa_length": 1362,
"cds_start": 3980,
"cds_end": null,
"cds_length": 4089,
"cdna_start": 4069,
"cdna_end": null,
"cdna_length": 4271,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3980A>C",
"hgvs_p": "p.Lys1327Thr",
"transcript": "ENST00000700002.1",
"protein_id": "ENSP00000514750.1",
"transcript_support_level": null,
"aa_start": 1327,
"aa_end": null,
"aa_length": 1362,
"cds_start": 3980,
"cds_end": null,
"cds_length": 4089,
"cdna_start": 4052,
"cdna_end": null,
"cdna_length": 4233,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3974A>C",
"hgvs_p": "p.Lys1325Thr",
"transcript": "NM_001406796.1",
"protein_id": "NP_001393725.1",
"transcript_support_level": null,
"aa_start": 1325,
"aa_end": null,
"aa_length": 1360,
"cds_start": 3974,
"cds_end": null,
"cds_length": 4083,
"cdna_start": 4063,
"cdna_end": null,
"cdna_length": 4315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3974A>C",
"hgvs_p": "p.Lys1325Thr",
"transcript": "NM_001406809.1",
"protein_id": "NP_001393738.1",
"transcript_support_level": null,
"aa_start": 1325,
"aa_end": null,
"aa_length": 1360,
"cds_start": 3974,
"cds_end": null,
"cds_length": 4083,
"cdna_start": 4063,
"cdna_end": null,
"cdna_length": 4318,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3974A>C",
"hgvs_p": "p.Lys1325Thr",
"transcript": "NM_001406808.1",
"protein_id": "NP_001393737.1",
"transcript_support_level": null,
"aa_start": 1325,
"aa_end": null,
"aa_length": 1337,
"cds_start": 3974,
"cds_end": null,
"cds_length": 4014,
"cdna_start": 4063,
"cdna_end": null,
"cdna_length": 4260,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3896A>C",
"hgvs_p": "p.Lys1299Thr",
"transcript": "NM_001406804.1",
"protein_id": "NP_001393733.1",
"transcript_support_level": null,
"aa_start": 1299,
"aa_end": null,
"aa_length": 1334,
"cds_start": 3896,
"cds_end": null,
"cds_length": 4005,
"cdna_start": 4040,
"cdna_end": null,
"cdna_length": 4242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3806A>C",
"hgvs_p": "p.Lys1269Thr",
"transcript": "NM_001406826.1",
"protein_id": "NP_001393755.1",
"transcript_support_level": null,
"aa_start": 1269,
"aa_end": null,
"aa_length": 1304,
"cds_start": 3806,
"cds_end": null,
"cds_length": 3915,
"cdna_start": 4186,
"cdna_end": null,
"cdna_length": 4388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3800A>C",
"hgvs_p": "p.Lys1267Thr",
"transcript": "NM_001406798.1",
"protein_id": "NP_001393727.1",
"transcript_support_level": null,
"aa_start": 1267,
"aa_end": null,
"aa_length": 1302,
"cds_start": 3800,
"cds_end": null,
"cds_length": 3909,
"cdna_start": 3889,
"cdna_end": null,
"cdna_length": 4091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3677A>C",
"hgvs_p": "p.Lys1226Thr",
"transcript": "NM_001406797.1",
"protein_id": "NP_001393726.1",
"transcript_support_level": null,
"aa_start": 1226,
"aa_end": null,
"aa_length": 1261,
"cds_start": 3677,
"cds_end": null,
"cds_length": 3786,
"cdna_start": 3801,
"cdna_end": null,
"cdna_length": 4003,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3677A>C",
"hgvs_p": "p.Lys1226Thr",
"transcript": "NM_001406805.1",
"protein_id": "NP_001393734.1",
"transcript_support_level": null,
"aa_start": 1226,
"aa_end": null,
"aa_length": 1261,
"cds_start": 3677,
"cds_end": null,
"cds_length": 3786,
"cdna_start": 3801,
"cdna_end": null,
"cdna_length": 4053,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3677A>C",
"hgvs_p": "p.Lys1226Thr",
"transcript": "NM_001406818.1",
"protein_id": "NP_001393747.1",
"transcript_support_level": null,
"aa_start": 1226,
"aa_end": null,
"aa_length": 1261,
"cds_start": 3677,
"cds_end": null,
"cds_length": 3786,
"cdna_start": 3891,
"cdna_end": null,
"cdna_length": 4093,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3677A>C",
"hgvs_p": "p.Lys1226Thr",
"transcript": "NM_001406819.1",
"protein_id": "NP_001393748.1",
"transcript_support_level": null,
"aa_start": 1226,
"aa_end": null,
"aa_length": 1261,
"cds_start": 3677,
"cds_end": null,
"cds_length": 3786,
"cdna_start": 3867,
"cdna_end": null,
"cdna_length": 4069,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3677A>C",
"hgvs_p": "p.Lys1226Thr",
"transcript": "NM_001406820.1",
"protein_id": "NP_001393749.1",
"transcript_support_level": null,
"aa_start": 1226,
"aa_end": null,
"aa_length": 1261,
"cds_start": 3677,
"cds_end": null,
"cds_length": 3786,
"cdna_start": 3768,
"cdna_end": null,
"cdna_length": 3970,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3677A>C",
"hgvs_p": "p.Lys1226Thr",
"transcript": "NM_001406821.1",
"protein_id": "NP_001393750.1",
"transcript_support_level": null,
"aa_start": 1226,
"aa_end": null,
"aa_length": 1261,
"cds_start": 3677,
"cds_end": null,
"cds_length": 3786,
"cdna_start": 3867,
"cdna_end": null,
"cdna_length": 4119,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3677A>C",
"hgvs_p": "p.Lys1226Thr",
"transcript": "NM_001406824.1",
"protein_id": "NP_001393753.1",
"transcript_support_level": null,
"aa_start": 1226,
"aa_end": null,
"aa_length": 1261,
"cds_start": 3677,
"cds_end": null,
"cds_length": 3786,
"cdna_start": 3864,
"cdna_end": null,
"cdna_length": 4066,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3677A>C",
"hgvs_p": "p.Lys1226Thr",
"transcript": "NM_001406825.1",
"protein_id": "NP_001393754.1",
"transcript_support_level": null,
"aa_start": 1226,
"aa_end": null,
"aa_length": 1261,
"cds_start": 3677,
"cds_end": null,
"cds_length": 3786,
"cdna_start": 3963,
"cdna_end": null,
"cdna_length": 4165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3677A>C",
"hgvs_p": "p.Lys1226Thr",
"transcript": "NM_001406827.1",
"protein_id": "NP_001393756.1",
"transcript_support_level": null,
"aa_start": 1226,
"aa_end": null,
"aa_length": 1261,
"cds_start": 3677,
"cds_end": null,
"cds_length": 3786,
"cdna_start": 3797,
"cdna_end": null,
"cdna_length": 3999,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
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{
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}
],
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"allele_count_reference_population": 1,
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"gnomad_exomes_ac": 1,
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"gnomad_exomes_homalt": 0,
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"gnomad_mito_homoplasmic": null,
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"computational_score_selected": 0.3473607301712036,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1077,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 0.746,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
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"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM2,BP4",
"acmg_by_gene": [
{
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"benign_score": 1,
"pathogenic_score": 4,
"criteria": [
"PM1",
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000179.3",
"gene_symbol": "MSH6",
"hgnc_id": 7329,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3974A>C",
"hgvs_p": "p.Lys1325Thr"
},
{
"score": 1,
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"criteria": [
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"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000682451.1",
"gene_symbol": "FBXO11",
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"effects": [
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],
"inheritance_mode": "AD",
"hgvs_c": "n.4124T>G",
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}
],
"clinvar_disease": " 1, familial, susceptibility to,Breast-ovarian cancer,Hereditary cancer-predisposing syndrome,Hereditary nonpolyposis colorectal neoplasms",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Hereditary nonpolyposis colorectal neoplasms|Hereditary cancer-predisposing syndrome|Breast-ovarian cancer, familial, susceptibility to, 1",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}