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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: X-107645193-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=107645193&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 107645193,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000372435.10",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.547G>C",
"hgvs_p": "p.Asp183His",
"transcript": "NM_002764.4",
"protein_id": "NP_002755.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 318,
"cds_start": 547,
"cds_end": null,
"cds_length": 957,
"cdna_start": 666,
"cdna_end": null,
"cdna_length": 2070,
"mane_select": "ENST00000372435.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.547G>C",
"hgvs_p": "p.Asp183His",
"transcript": "ENST00000372435.10",
"protein_id": "ENSP00000361512.4",
"transcript_support_level": 1,
"aa_start": 183,
"aa_end": null,
"aa_length": 318,
"cds_start": 547,
"cds_end": null,
"cds_length": 957,
"cdna_start": 666,
"cdna_end": null,
"cdna_length": 2070,
"mane_select": "NM_002764.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.547G>C",
"hgvs_p": "p.Asp183His",
"transcript": "ENST00000643795.2",
"protein_id": "ENSP00000496286.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 321,
"cds_start": 547,
"cds_end": null,
"cds_length": 966,
"cdna_start": 748,
"cdna_end": null,
"cdna_length": 1450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"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": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.448G>C",
"hgvs_p": "p.Asp150His",
"transcript": "ENST00000372418.4",
"protein_id": "ENSP00000361495.2",
"transcript_support_level": 3,
"aa_start": 150,
"aa_end": null,
"aa_length": 285,
"cds_start": 448,
"cds_end": null,
"cds_length": 858,
"cdna_start": 587,
"cdna_end": null,
"cdna_length": 1434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.16G>C",
"hgvs_p": "p.Asp6His",
"transcript": "ENST00000675875.1",
"protein_id": "ENSP00000502070.1",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 48,
"cds_start": 16,
"cds_end": null,
"cds_length": 147,
"cdna_start": 17,
"cdna_end": null,
"cdna_length": 431,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*16G>C",
"hgvs_p": null,
"transcript": "ENST00000644642.1",
"protein_id": "ENSP00000495493.1",
"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": 1515,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.507G>C",
"hgvs_p": null,
"transcript": "ENST00000674525.1",
"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": 883,
"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": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*240G>C",
"hgvs_p": null,
"transcript": "ENST00000674826.1",
"protein_id": "ENSP00000502278.1",
"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": 996,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.200G>C",
"hgvs_p": null,
"transcript": "ENST00000675046.1",
"protein_id": "ENSP00000501767.1",
"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": 518,
"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": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*12G>C",
"hgvs_p": null,
"transcript": "ENST00000675124.1",
"protein_id": "ENSP00000502439.1",
"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": 527,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.16G>C",
"hgvs_p": null,
"transcript": "ENST00000675353.1",
"protein_id": "ENSP00000502149.1",
"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": 549,
"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": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*47G>C",
"hgvs_p": null,
"transcript": "ENST00000675630.1",
"protein_id": "ENSP00000502050.1",
"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": 523,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*131G>C",
"hgvs_p": null,
"transcript": "ENST00000675720.1",
"protein_id": "ENSP00000501721.1",
"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": 580,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.16G>C",
"hgvs_p": null,
"transcript": "ENST00000676365.1",
"protein_id": "ENSP00000501550.1",
"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": 525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.-66G>C",
"hgvs_p": null,
"transcript": "NM_001204402.2",
"protein_id": "NP_001191331.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 114,
"cds_start": -4,
"cds_end": null,
"cds_length": 345,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1662,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*16G>C",
"hgvs_p": null,
"transcript": "ENST00000644642.1",
"protein_id": "ENSP00000495493.1",
"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": 1515,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*240G>C",
"hgvs_p": null,
"transcript": "ENST00000674826.1",
"protein_id": "ENSP00000502278.1",
"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": 996,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*12G>C",
"hgvs_p": null,
"transcript": "ENST00000675124.1",
"protein_id": "ENSP00000502439.1",
"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": 527,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*47G>C",
"hgvs_p": null,
"transcript": "ENST00000675630.1",
"protein_id": "ENSP00000502050.1",
"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": 523,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "n.*131G>C",
"hgvs_p": null,
"transcript": "ENST00000675720.1",
"protein_id": "ENSP00000501721.1",
"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": 580,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.358+4240G>C",
"hgvs_p": null,
"transcript": "ENST00000676092.1",
"protein_id": "ENSP00000502780.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 121,
"cds_start": -4,
"cds_end": null,
"cds_length": 366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 487,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.126-2413G>C",
"hgvs_p": null,
"transcript": "ENST00000675082.1",
"protein_id": "ENSP00000502347.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 94,
"cds_start": -4,
"cds_end": null,
"cds_length": 285,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"hgvs_c": "c.126-5G>C",
"hgvs_p": null,
"transcript": "ENST00000675921.1",
"protein_id": "ENSP00000502707.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 91,
"cds_start": -4,
"cds_end": null,
"cds_length": 278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 278,
"mane_select": null,
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"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 3,
"intron_rank": 2,
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"gene_symbol": "ENSG00000289923",
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"hgvs_c": "n.359-2068C>G",
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"transcript": "ENST00000723190.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cds_length": null,
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"cdna_length": 560,
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"biotype": null,
"feature": null
}
],
"gene_symbol": "PRPS1",
"gene_hgnc_id": 9462,
"dbsnp": "rs137852541",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9593244791030884,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.965,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9958,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.65,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.478,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000372435.10",
"gene_symbol": "PRPS1",
"hgnc_id": 9462,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.547G>C",
"hgvs_p": "p.Asp183His"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000723190.1",
"gene_symbol": "ENSG00000289923",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.359-2068C>G",
"hgvs_p": null
}
],
"clinvar_disease": "Arts syndrome,Phosphoribosylpyrophosphate synthetase superactivity",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Phosphoribosylpyrophosphate synthetase superactivity|Arts syndrome",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}