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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: 12-109058045-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=109058045&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 109058045,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_032663.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "NM_032663.5",
"protein_id": "NP_116052.2",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 517,
"cds_start": 313,
"cds_end": null,
"cds_length": 1554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000257548.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032663.5"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "ENST00000257548.10",
"protein_id": "ENSP00000257548.5",
"transcript_support_level": 1,
"aa_start": 105,
"aa_end": null,
"aa_length": 517,
"cds_start": 313,
"cds_end": null,
"cds_length": 1554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032663.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000257548.10"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "ENST00000928066.1",
"protein_id": "ENSP00000598125.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 554,
"cds_start": 313,
"cds_end": null,
"cds_length": 1665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000928066.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "ENST00000962121.1",
"protein_id": "ENSP00000632180.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 550,
"cds_start": 313,
"cds_end": null,
"cds_length": 1653,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962121.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "ENST00000928067.1",
"protein_id": "ENSP00000598126.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 526,
"cds_start": 313,
"cds_end": null,
"cds_length": 1581,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000928067.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "ENST00000910054.1",
"protein_id": "ENSP00000580113.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 516,
"cds_start": 313,
"cds_end": null,
"cds_length": 1551,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910054.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "ENST00000910056.1",
"protein_id": "ENSP00000580115.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 507,
"cds_start": 313,
"cds_end": null,
"cds_length": 1524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910056.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "ENST00000962122.1",
"protein_id": "ENSP00000632181.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 497,
"cds_start": 313,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962122.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "ENST00000910055.1",
"protein_id": "ENSP00000580114.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 490,
"cds_start": 313,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910055.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "ENST00000928065.1",
"protein_id": "ENSP00000598124.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 488,
"cds_start": 313,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000928065.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.220A>G",
"hgvs_p": "p.Arg74Gly",
"transcript": "NM_001301175.2",
"protein_id": "NP_001288104.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 486,
"cds_start": 220,
"cds_end": null,
"cds_length": 1461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001301175.2"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.220A>G",
"hgvs_p": "p.Arg74Gly",
"transcript": "ENST00000392784.6",
"protein_id": "ENSP00000376535.2",
"transcript_support_level": 2,
"aa_start": 74,
"aa_end": null,
"aa_length": 486,
"cds_start": 220,
"cds_end": null,
"cds_length": 1461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392784.6"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "ENST00000910057.1",
"protein_id": "ENSP00000580116.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 437,
"cds_start": 313,
"cds_end": null,
"cds_length": 1314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910057.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.220A>G",
"hgvs_p": "p.Arg74Gly",
"transcript": "ENST00000536723.5",
"protein_id": "ENSP00000443678.1",
"transcript_support_level": 5,
"aa_start": 74,
"aa_end": null,
"aa_length": 176,
"cds_start": 220,
"cds_end": null,
"cds_length": 532,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000536723.5"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.235A>G",
"hgvs_p": "p.Arg79Gly",
"transcript": "ENST00000539121.1",
"protein_id": "ENSP00000440837.1",
"transcript_support_level": 4,
"aa_start": 79,
"aa_end": null,
"aa_length": 94,
"cds_start": 235,
"cds_end": null,
"cds_length": 286,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000539121.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "XM_017020048.2",
"protein_id": "XP_016875537.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 554,
"cds_start": 313,
"cds_end": null,
"cds_length": 1665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017020048.2"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "XM_017020049.2",
"protein_id": "XP_016875538.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 553,
"cds_start": 313,
"cds_end": null,
"cds_length": 1662,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017020049.2"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.220A>G",
"hgvs_p": "p.Arg74Gly",
"transcript": "XM_017020050.2",
"protein_id": "XP_016875539.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 523,
"cds_start": 220,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017020050.2"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.220A>G",
"hgvs_p": "p.Arg74Gly",
"transcript": "XM_017020051.3",
"protein_id": "XP_016875540.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 523,
"cds_start": 220,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017020051.3"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.220A>G",
"hgvs_p": "p.Arg74Gly",
"transcript": "XM_017020052.3",
"protein_id": "XP_016875541.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 523,
"cds_start": 220,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017020052.3"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.220A>G",
"hgvs_p": "p.Arg74Gly",
"transcript": "XM_047429732.1",
"protein_id": "XP_047285688.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 523,
"cds_start": 220,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429732.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP30",
"gene_hgnc_id": 20065,
"hgvs_c": "c.313A>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "XM_005253962.4",
"protein_id": "XP_005254019.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 516,
"cds_start": 313,
"cds_end": null,
"cds_length": 1551,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005253962.4"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
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{
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},
{
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],
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"gene_symbol": "USP30",
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"hgvs_c": "n.83+5284A>G",
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"transcript": "ENST00000377883.7",
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"biotype": "nonsense_mediated_decay",
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],
"gene_symbol": "USP30",
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"dbsnp": "rs773464619",
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"hom_count_reference_population": 0,
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"gnomad_exomes_af": 0.0000588285,
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"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
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"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06500864028930664,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.063,
"revel_prediction": "Benign",
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"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.623,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
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"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_032663.5",
"gene_symbol": "USP30",
"hgnc_id": 20065,
"effects": [
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],
"inheritance_mode": "AR",
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"hgvs_p": "p.Arg105Gly"
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],
"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
}