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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: 1-113830026-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=113830026&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 113830026,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000359785.10",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.2057T>C",
"hgvs_p": "p.Leu686Pro",
"transcript": "ENST00000359785.10",
"protein_id": "ENSP00000352833.5",
"transcript_support_level": 1,
"aa_start": 686,
"aa_end": null,
"aa_length": 807,
"cds_start": 2057,
"cds_end": null,
"cds_length": 2424,
"cdna_start": 2146,
"cdna_end": null,
"cdna_length": 3607,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.2057T>C",
"hgvs_p": "p.Leu686Pro",
"transcript": "ENST00000420377.6",
"protein_id": "ENSP00000388229.2",
"transcript_support_level": 1,
"aa_start": 686,
"aa_end": null,
"aa_length": 795,
"cds_start": 2057,
"cds_end": null,
"cds_length": 2388,
"cdna_start": 2146,
"cdna_end": null,
"cdna_length": 2726,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1985T>C",
"hgvs_p": "p.Leu662Pro",
"transcript": "ENST00000538253.5",
"protein_id": "ENSP00000439372.2",
"transcript_support_level": 1,
"aa_start": 662,
"aa_end": null,
"aa_length": 783,
"cds_start": 1985,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 2115,
"cdna_end": null,
"cdna_length": 3575,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1892T>C",
"hgvs_p": "p.Leu631Pro",
"transcript": "ENST00000528414.5",
"protein_id": "ENSP00000435176.1",
"transcript_support_level": 1,
"aa_start": 631,
"aa_end": null,
"aa_length": 752,
"cds_start": 1892,
"cds_end": null,
"cds_length": 2259,
"cdna_start": 1967,
"cdna_end": null,
"cdna_length": 3424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1676T>C",
"hgvs_p": "p.Leu559Pro",
"transcript": "ENST00000525799.1",
"protein_id": "ENSP00000432674.1",
"transcript_support_level": 1,
"aa_start": 559,
"aa_end": null,
"aa_length": 668,
"cds_start": 1676,
"cds_end": null,
"cds_length": 2007,
"cdna_start": 1765,
"cdna_end": null,
"cdna_length": 2118,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.469-10372T>C",
"hgvs_p": null,
"transcript": "ENST00000460620.5",
"protein_id": "ENSP00000433141.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 179,
"cds_start": -4,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.2057T>C",
"hgvs_p": "p.Leu686Pro",
"transcript": "NM_015967.8",
"protein_id": "NP_057051.4",
"transcript_support_level": null,
"aa_start": 686,
"aa_end": null,
"aa_length": 807,
"cds_start": 2057,
"cds_end": null,
"cds_length": 2424,
"cdna_start": 2146,
"cdna_end": null,
"cdna_length": 3607,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1985T>C",
"hgvs_p": "p.Leu662Pro",
"transcript": "NM_001308297.2",
"protein_id": "NP_001295226.2",
"transcript_support_level": null,
"aa_start": 662,
"aa_end": null,
"aa_length": 783,
"cds_start": 1985,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 2074,
"cdna_end": null,
"cdna_length": 3535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1973T>C",
"hgvs_p": "p.Leu658Pro",
"transcript": "NM_001193431.3",
"protein_id": "NP_001180360.2",
"transcript_support_level": null,
"aa_start": 658,
"aa_end": null,
"aa_length": 779,
"cds_start": 1973,
"cds_end": null,
"cds_length": 2340,
"cdna_start": 2062,
"cdna_end": null,
"cdna_length": 3523,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1892T>C",
"hgvs_p": "p.Leu631Pro",
"transcript": "NM_012411.6",
"protein_id": "NP_036543.5",
"transcript_support_level": null,
"aa_start": 631,
"aa_end": null,
"aa_length": 752,
"cds_start": 1892,
"cds_end": null,
"cds_length": 2259,
"cdna_start": 1981,
"cdna_end": null,
"cdna_length": 3442,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1979T>C",
"hgvs_p": "p.Leu660Pro",
"transcript": "XM_011541221.2",
"protein_id": "XP_011539523.1",
"transcript_support_level": null,
"aa_start": 660,
"aa_end": null,
"aa_length": 781,
"cds_start": 1979,
"cds_end": null,
"cds_length": 2346,
"cdna_start": 2115,
"cdna_end": null,
"cdna_length": 3576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.2057T>C",
"hgvs_p": "p.Leu686Pro",
"transcript": "XM_011541222.2",
"protein_id": "XP_011539524.1",
"transcript_support_level": null,
"aa_start": 686,
"aa_end": null,
"aa_length": 773,
"cds_start": 2057,
"cds_end": null,
"cds_length": 2322,
"cdna_start": 2193,
"cdna_end": null,
"cdna_length": 3623,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1907T>C",
"hgvs_p": "p.Leu636Pro",
"transcript": "XM_047417630.1",
"protein_id": "XP_047273586.1",
"transcript_support_level": null,
"aa_start": 636,
"aa_end": null,
"aa_length": 757,
"cds_start": 1907,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 2043,
"cdna_end": null,
"cdna_length": 3504,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1901T>C",
"hgvs_p": "p.Leu634Pro",
"transcript": "XM_047417631.1",
"protein_id": "XP_047273587.1",
"transcript_support_level": null,
"aa_start": 634,
"aa_end": null,
"aa_length": 755,
"cds_start": 1901,
"cds_end": null,
"cds_length": 2268,
"cdna_start": 2037,
"cdna_end": null,
"cdna_length": 3498,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1895T>C",
"hgvs_p": "p.Leu632Pro",
"transcript": "XM_047417632.1",
"protein_id": "XP_047273588.1",
"transcript_support_level": null,
"aa_start": 632,
"aa_end": null,
"aa_length": 753,
"cds_start": 1895,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 2031,
"cdna_end": null,
"cdna_length": 3492,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1985T>C",
"hgvs_p": "p.Leu662Pro",
"transcript": "XM_011541225.3",
"protein_id": "XP_011539527.1",
"transcript_support_level": null,
"aa_start": 662,
"aa_end": null,
"aa_length": 749,
"cds_start": 1985,
"cds_end": null,
"cds_length": 2250,
"cdna_start": 2121,
"cdna_end": null,
"cdna_length": 3551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1712T>C",
"hgvs_p": "p.Leu571Pro",
"transcript": "XM_017001005.3",
"protein_id": "XP_016856494.1",
"transcript_support_level": null,
"aa_start": 571,
"aa_end": null,
"aa_length": 692,
"cds_start": 1712,
"cds_end": null,
"cds_length": 2079,
"cdna_start": 2050,
"cdna_end": null,
"cdna_length": 3511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "n.*1335T>C",
"hgvs_p": null,
"transcript": "ENST00000532224.5",
"protein_id": "ENSP00000431249.1",
"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": 2421,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "n.*1335T>C",
"hgvs_p": null,
"transcript": "ENST00000532224.5",
"protein_id": "ENSP00000431249.1",
"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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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "AP4B1-AS1",
"gene_hgnc_id": 44114,
"hgvs_c": "n.419-1736A>G",
"hgvs_p": null,
"transcript": "ENST00000664434.1",
"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": 802,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "AP4B1-AS1",
"gene_hgnc_id": 44114,
"hgvs_c": "n.440+14554A>G",
"hgvs_p": null,
"transcript": "ENST00000717022.1",
"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": 1566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "AP4B1-AS1",
"gene_hgnc_id": 44114,
"hgvs_c": "n.383+14554A>G",
"hgvs_p": null,
"transcript": "ENST00000836797.1",
"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": 681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "AP4B1-AS1",
"gene_hgnc_id": 44114,
"hgvs_c": "n.414+14554A>G",
"hgvs_p": null,
"transcript": "NR_125965.1",
"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": 1902,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.*1559T>C",
"hgvs_p": null,
"transcript": "XM_011541223.3",
"protein_id": "XP_011539525.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 715,
"cds_start": -4,
"cds_end": null,
"cds_length": 2148,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"dbsnp": "rs771396787",
"frequency_reference_population": 0.0000013890992,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.0000013891,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04035532474517822,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.019,
"revel_prediction": "Benign",
"alphamissense_score": 0.0657,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.021,
"phylop100way_prediction": "Benign",
"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": -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": "ENST00000359785.10",
"gene_symbol": "PTPN22",
"hgnc_id": 9652,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AR",
"hgvs_c": "c.2057T>C",
"hgvs_p": "p.Leu686Pro"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NR_125965.1",
"gene_symbol": "AP4B1-AS1",
"hgnc_id": 44114,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.414+14554A>G",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}