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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-53241890-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=53241890&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 53241890,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000642864.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2909G>A",
"hgvs_p": "p.Arg970His",
"transcript": "NM_001111125.3",
"protein_id": "NP_001104595.1",
"transcript_support_level": null,
"aa_start": 970,
"aa_end": null,
"aa_length": 1488,
"cds_start": 2909,
"cds_end": null,
"cds_length": 4467,
"cdna_start": 3136,
"cdna_end": null,
"cdna_length": 6037,
"mane_select": "ENST00000642864.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2909G>A",
"hgvs_p": "p.Arg970His",
"transcript": "ENST00000642864.1",
"protein_id": "ENSP00000495726.1",
"transcript_support_level": null,
"aa_start": 970,
"aa_end": null,
"aa_length": 1488,
"cds_start": 2909,
"cds_end": null,
"cds_length": 4467,
"cdna_start": 3136,
"cdna_end": null,
"cdna_length": 6037,
"mane_select": "NM_001111125.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2294G>A",
"hgvs_p": "p.Arg765His",
"transcript": "ENST00000375365.2",
"protein_id": "ENSP00000364514.2",
"transcript_support_level": 1,
"aa_start": 765,
"aa_end": null,
"aa_length": 949,
"cds_start": 2294,
"cds_end": null,
"cds_length": 2850,
"cdna_start": 2387,
"cdna_end": null,
"cdna_length": 4004,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3068G>A",
"hgvs_p": "p.Arg1023His",
"transcript": "ENST00000706952.1",
"protein_id": "ENSP00000516672.1",
"transcript_support_level": null,
"aa_start": 1023,
"aa_end": null,
"aa_length": 1541,
"cds_start": 3068,
"cds_end": null,
"cds_length": 4626,
"cdna_start": 3068,
"cdna_end": null,
"cdna_length": 5969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2909G>A",
"hgvs_p": "p.Arg970His",
"transcript": "ENST00000674510.1",
"protein_id": "ENSP00000502054.1",
"transcript_support_level": null,
"aa_start": 970,
"aa_end": null,
"aa_length": 1488,
"cds_start": 2909,
"cds_end": null,
"cds_length": 4467,
"cdna_start": 3110,
"cdna_end": null,
"cdna_length": 6011,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2879G>A",
"hgvs_p": "p.Arg960His",
"transcript": "ENST00000675719.1",
"protein_id": "ENSP00000501927.1",
"transcript_support_level": null,
"aa_start": 960,
"aa_end": null,
"aa_length": 1478,
"cds_start": 2879,
"cds_end": null,
"cds_length": 4437,
"cdna_start": 3106,
"cdna_end": null,
"cdna_length": 6008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2909G>A",
"hgvs_p": "p.Arg970His",
"transcript": "NM_001441092.1",
"protein_id": "NP_001428021.1",
"transcript_support_level": null,
"aa_start": 970,
"aa_end": null,
"aa_length": 1168,
"cds_start": 2909,
"cds_end": null,
"cds_length": 3507,
"cdna_start": 3136,
"cdna_end": null,
"cdna_length": 7654,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2909G>A",
"hgvs_p": "p.Arg970His",
"transcript": "NM_001410736.1",
"protein_id": "NP_001397665.1",
"transcript_support_level": null,
"aa_start": 970,
"aa_end": null,
"aa_length": 1154,
"cds_start": 2909,
"cds_end": null,
"cds_length": 3465,
"cdna_start": 3136,
"cdna_end": null,
"cdna_length": 5987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2909G>A",
"hgvs_p": "p.Arg970His",
"transcript": "ENST00000640694.1",
"protein_id": "ENSP00000492403.1",
"transcript_support_level": 5,
"aa_start": 970,
"aa_end": null,
"aa_length": 1154,
"cds_start": 2909,
"cds_end": null,
"cds_length": 3465,
"cdna_start": 3105,
"cdna_end": null,
"cdna_length": 5958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2411G>A",
"hgvs_p": "p.Arg804His",
"transcript": "NM_001441093.1",
"protein_id": "NP_001428022.1",
"transcript_support_level": null,
"aa_start": 804,
"aa_end": null,
"aa_length": 988,
"cds_start": 2411,
"cds_end": null,
"cds_length": 2967,
"cdna_start": 2474,
"cdna_end": null,
"cdna_length": 5325,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2294G>A",
"hgvs_p": "p.Arg765His",
"transcript": "NM_015075.2",
"protein_id": "NP_055890.1",
"transcript_support_level": null,
"aa_start": 765,
"aa_end": null,
"aa_length": 949,
"cds_start": 2294,
"cds_end": null,
"cds_length": 2850,
"cdna_start": 2357,
"cdna_end": null,
"cdna_length": 5208,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"transcript": "NM_001441095.1",
"protein_id": "NP_001428024.1",
"transcript_support_level": null,
"aa_start": 733,
"aa_end": null,
"aa_length": 931,
"cds_start": 2198,
"cds_end": null,
"cds_length": 2796,
"cdna_start": 2261,
"cdna_end": null,
"cdna_length": 6779,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"transcript": "NM_001441094.1",
"protein_id": "NP_001428023.1",
"transcript_support_level": null,
"aa_start": 733,
"aa_end": null,
"aa_length": 917,
"cds_start": 2198,
"cds_end": null,
"cds_length": 2754,
"cdna_start": 2261,
"cdna_end": null,
"cdna_length": 5112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.860G>A",
"hgvs_p": "p.Arg287His",
"transcript": "ENST00000638521.1",
"protein_id": "ENSP00000492636.1",
"transcript_support_level": 5,
"aa_start": 287,
"aa_end": null,
"aa_length": 529,
"cds_start": 860,
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"cds_length": 1590,
"cdna_start": 861,
"cdna_end": null,
"cdna_length": 4501,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.368G>A",
"hgvs_p": "p.Arg123His",
"transcript": "ENST00000638869.1",
"protein_id": "ENSP00000491736.1",
"transcript_support_level": 5,
"aa_start": 123,
"aa_end": null,
"aa_length": 333,
"cds_start": 368,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 370,
"cdna_end": null,
"cdna_length": 3000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3005G>A",
"hgvs_p": "p.Arg1002His",
"transcript": "XM_006724579.4",
"protein_id": "XP_006724642.1",
"transcript_support_level": null,
"aa_start": 1002,
"aa_end": null,
"aa_length": 1520,
"cds_start": 3005,
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"cdna_start": 3232,
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"cdna_length": 6133,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2411G>A",
"hgvs_p": "p.Arg804His",
"transcript": "XM_017029360.2",
"protein_id": "XP_016884849.1",
"transcript_support_level": null,
"aa_start": 804,
"aa_end": null,
"aa_length": 1322,
"cds_start": 2411,
"cds_end": null,
"cds_length": 3969,
"cdna_start": 2474,
"cdna_end": null,
"cdna_length": 5375,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2294G>A",
"hgvs_p": "p.Arg765His",
"transcript": "XM_006724580.4",
"protein_id": "XP_006724643.1",
"transcript_support_level": null,
"aa_start": 765,
"aa_end": null,
"aa_length": 1283,
"cds_start": 2294,
"cds_end": null,
"cds_length": 3852,
"cdna_start": 2357,
"cdna_end": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"transcript": "XM_011530773.3",
"protein_id": "XP_011529075.1",
"transcript_support_level": null,
"aa_start": 733,
"aa_end": null,
"aa_length": 1251,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "R",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3005G>A",
"hgvs_p": "p.Arg1002His",
"transcript": "XM_006724581.5",
"protein_id": "XP_006724644.1",
"transcript_support_level": null,
"aa_start": 1002,
"aa_end": null,
"aa_length": 1244,
"cds_start": 3005,
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"cdna_start": 3232,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3005G>A",
"hgvs_p": "p.Arg1002His",
"transcript": "XM_011530774.4",
"protein_id": "XP_011529076.1",
"transcript_support_level": null,
"aa_start": 1002,
"aa_end": null,
"aa_length": 1222,
"cds_start": 3005,
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"cdna_start": 3232,
"cdna_end": null,
"cdna_length": 4167,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3005G>A",
"hgvs_p": "p.Arg1002His",
"transcript": "XM_006724582.5",
"protein_id": "XP_006724645.1",
"transcript_support_level": null,
"aa_start": 1002,
"aa_end": null,
"aa_length": 1212,
"cds_start": 3005,
"cds_end": null,
"cds_length": 3639,
"cdna_start": 3232,
"cdna_end": null,
"cdna_length": 5877,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
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{
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],
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},
{
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],
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"gene_symbol": "IQSEC2",
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"transcript": "ENST00000640005.1",
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}
],
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"dbsnp": "rs1556860937",
"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": 0.8309445381164551,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.736,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9513,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.15,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.898,
"phylop100way_prediction": "Pathogenic",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000642864.1",
"gene_symbol": "IQSEC2",
"hgnc_id": 29059,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.2909G>A",
"hgvs_p": "p.Arg970His"
}
],
"clinvar_disease": " X-linked 1,Inborn genetic diseases,Intellectual disability,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Intellectual disability, X-linked 1|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}