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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: 3-49278426-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49278426&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 49278426,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_003363.4",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2759A>G",
"hgvs_p": "p.Tyr920Cys",
"transcript": "NM_003363.4",
"protein_id": "NP_003354.2",
"transcript_support_level": null,
"aa_start": 920,
"aa_end": null,
"aa_length": 963,
"cds_start": 2759,
"cds_end": null,
"cds_length": 2892,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000265560.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003363.4"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2759A>G",
"hgvs_p": "p.Tyr920Cys",
"transcript": "ENST00000265560.9",
"protein_id": "ENSP00000265560.4",
"transcript_support_level": 1,
"aa_start": 920,
"aa_end": null,
"aa_length": 963,
"cds_start": 2759,
"cds_end": null,
"cds_length": 2892,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003363.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000265560.9"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2618A>G",
"hgvs_p": "p.Tyr873Cys",
"transcript": "ENST00000351842.8",
"protein_id": "ENSP00000341028.4",
"transcript_support_level": 1,
"aa_start": 873,
"aa_end": null,
"aa_length": 916,
"cds_start": 2618,
"cds_end": null,
"cds_length": 2751,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000351842.8"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2912A>G",
"hgvs_p": "p.Tyr971Cys",
"transcript": "ENST00000911610.1",
"protein_id": "ENSP00000581669.1",
"transcript_support_level": null,
"aa_start": 971,
"aa_end": null,
"aa_length": 1014,
"cds_start": 2912,
"cds_end": null,
"cds_length": 3045,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911610.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2888A>G",
"hgvs_p": "p.Tyr963Cys",
"transcript": "ENST00000965332.1",
"protein_id": "ENSP00000635391.1",
"transcript_support_level": null,
"aa_start": 963,
"aa_end": null,
"aa_length": 1006,
"cds_start": 2888,
"cds_end": null,
"cds_length": 3021,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965332.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2870A>G",
"hgvs_p": "p.Tyr957Cys",
"transcript": "ENST00000965340.1",
"protein_id": "ENSP00000635399.1",
"transcript_support_level": null,
"aa_start": 957,
"aa_end": null,
"aa_length": 1000,
"cds_start": 2870,
"cds_end": null,
"cds_length": 3003,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965340.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2837A>G",
"hgvs_p": "p.Tyr946Cys",
"transcript": "ENST00000877491.1",
"protein_id": "ENSP00000547550.1",
"transcript_support_level": null,
"aa_start": 946,
"aa_end": null,
"aa_length": 989,
"cds_start": 2837,
"cds_end": null,
"cds_length": 2970,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877491.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2780A>G",
"hgvs_p": "p.Tyr927Cys",
"transcript": "ENST00000965341.1",
"protein_id": "ENSP00000635400.1",
"transcript_support_level": null,
"aa_start": 927,
"aa_end": null,
"aa_length": 970,
"cds_start": 2780,
"cds_end": null,
"cds_length": 2913,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965341.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2771A>G",
"hgvs_p": "p.Tyr924Cys",
"transcript": "ENST00000911611.1",
"protein_id": "ENSP00000581670.1",
"transcript_support_level": null,
"aa_start": 924,
"aa_end": null,
"aa_length": 967,
"cds_start": 2771,
"cds_end": null,
"cds_length": 2904,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911611.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2756A>G",
"hgvs_p": "p.Tyr919Cys",
"transcript": "ENST00000911612.1",
"protein_id": "ENSP00000581671.1",
"transcript_support_level": null,
"aa_start": 919,
"aa_end": null,
"aa_length": 962,
"cds_start": 2756,
"cds_end": null,
"cds_length": 2889,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911612.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2756A>G",
"hgvs_p": "p.Tyr919Cys",
"transcript": "ENST00000965324.1",
"protein_id": "ENSP00000635383.1",
"transcript_support_level": null,
"aa_start": 919,
"aa_end": null,
"aa_length": 962,
"cds_start": 2756,
"cds_end": null,
"cds_length": 2889,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965324.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2753A>G",
"hgvs_p": "p.Tyr918Cys",
"transcript": "ENST00000877475.1",
"protein_id": "ENSP00000547534.1",
"transcript_support_level": null,
"aa_start": 918,
"aa_end": null,
"aa_length": 961,
"cds_start": 2753,
"cds_end": null,
"cds_length": 2886,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877475.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2726A>G",
"hgvs_p": "p.Tyr909Cys",
"transcript": "ENST00000877488.1",
"protein_id": "ENSP00000547547.1",
"transcript_support_level": null,
"aa_start": 909,
"aa_end": null,
"aa_length": 952,
"cds_start": 2726,
"cds_end": null,
"cds_length": 2859,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877488.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2717A>G",
"hgvs_p": "p.Tyr906Cys",
"transcript": "ENST00000965327.1",
"protein_id": "ENSP00000635386.1",
"transcript_support_level": null,
"aa_start": 906,
"aa_end": null,
"aa_length": 949,
"cds_start": 2717,
"cds_end": null,
"cds_length": 2850,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965327.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2705A>G",
"hgvs_p": "p.Tyr902Cys",
"transcript": "ENST00000877477.1",
"protein_id": "ENSP00000547536.1",
"transcript_support_level": null,
"aa_start": 902,
"aa_end": null,
"aa_length": 945,
"cds_start": 2705,
"cds_end": null,
"cds_length": 2838,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877477.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2690A>G",
"hgvs_p": "p.Tyr897Cys",
"transcript": "ENST00000965330.1",
"protein_id": "ENSP00000635389.1",
"transcript_support_level": null,
"aa_start": 897,
"aa_end": null,
"aa_length": 940,
"cds_start": 2690,
"cds_end": null,
"cds_length": 2823,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965330.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2645A>G",
"hgvs_p": "p.Tyr882Cys",
"transcript": "ENST00000877480.1",
"protein_id": "ENSP00000547539.1",
"transcript_support_level": null,
"aa_start": 882,
"aa_end": null,
"aa_length": 925,
"cds_start": 2645,
"cds_end": null,
"cds_length": 2778,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877480.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2618A>G",
"hgvs_p": "p.Tyr873Cys",
"transcript": "NM_199443.3",
"protein_id": "NP_955475.1",
"transcript_support_level": null,
"aa_start": 873,
"aa_end": null,
"aa_length": 916,
"cds_start": 2618,
"cds_end": null,
"cds_length": 2751,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_199443.3"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2615A>G",
"hgvs_p": "p.Tyr872Cys",
"transcript": "ENST00000877484.1",
"protein_id": "ENSP00000547543.1",
"transcript_support_level": null,
"aa_start": 872,
"aa_end": null,
"aa_length": 915,
"cds_start": 2615,
"cds_end": null,
"cds_length": 2748,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877484.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2612A>G",
"hgvs_p": "p.Tyr871Cys",
"transcript": "ENST00000877485.1",
"protein_id": "ENSP00000547544.1",
"transcript_support_level": null,
"aa_start": 871,
"aa_end": null,
"aa_length": 914,
"cds_start": 2612,
"cds_end": null,
"cds_length": 2745,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877485.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2600A>G",
"hgvs_p": "p.Tyr867Cys",
"transcript": "ENST00000877473.1",
"protein_id": "ENSP00000547532.1",
"transcript_support_level": null,
"aa_start": 867,
"aa_end": null,
"aa_length": 910,
"cds_start": 2600,
"cds_end": null,
"cds_length": 2733,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877473.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2585A>G",
"hgvs_p": "p.Tyr862Cys",
"transcript": "ENST00000877492.1",
"protein_id": "ENSP00000547551.1",
"transcript_support_level": null,
"aa_start": 862,
"aa_end": null,
"aa_length": 905,
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{
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{
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{
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{
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{
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],
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{
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],
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{
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],
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"biotype": "retained_intron",
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],
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"dbsnp": "rs1313831176",
"frequency_reference_population": 0.0000013681444,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136814,
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"gnomad_exomes_ac": 2,
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"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9842606782913208,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.699,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9719,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.16,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.407,
"phylop100way_prediction": "Uncertain_significance",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
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"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_003363.4",
"gene_symbol": "USP4",
"hgnc_id": 12627,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2759A>G",
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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
}