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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: 3-49278312-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49278312&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 49278312,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_003363.4",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "Y",
"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.2873G>A",
"hgvs_p": "p.Cys958Tyr",
"transcript": "NM_003363.4",
"protein_id": "NP_003354.2",
"transcript_support_level": null,
"aa_start": 958,
"aa_end": null,
"aa_length": 963,
"cds_start": 2873,
"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": "C",
"aa_alt": "Y",
"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.2873G>A",
"hgvs_p": "p.Cys958Tyr",
"transcript": "ENST00000265560.9",
"protein_id": "ENSP00000265560.4",
"transcript_support_level": 1,
"aa_start": 958,
"aa_end": null,
"aa_length": 963,
"cds_start": 2873,
"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": "C",
"aa_alt": "Y",
"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.2732G>A",
"hgvs_p": "p.Cys911Tyr",
"transcript": "ENST00000351842.8",
"protein_id": "ENSP00000341028.4",
"transcript_support_level": 1,
"aa_start": 911,
"aa_end": null,
"aa_length": 916,
"cds_start": 2732,
"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": "C",
"aa_alt": "Y",
"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.3026G>A",
"hgvs_p": "p.Cys1009Tyr",
"transcript": "ENST00000911610.1",
"protein_id": "ENSP00000581669.1",
"transcript_support_level": null,
"aa_start": 1009,
"aa_end": null,
"aa_length": 1014,
"cds_start": 3026,
"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": "C",
"aa_alt": "Y",
"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.3002G>A",
"hgvs_p": "p.Cys1001Tyr",
"transcript": "ENST00000965332.1",
"protein_id": "ENSP00000635391.1",
"transcript_support_level": null,
"aa_start": 1001,
"aa_end": null,
"aa_length": 1006,
"cds_start": 3002,
"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": "C",
"aa_alt": "Y",
"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.2984G>A",
"hgvs_p": "p.Cys995Tyr",
"transcript": "ENST00000965340.1",
"protein_id": "ENSP00000635399.1",
"transcript_support_level": null,
"aa_start": 995,
"aa_end": null,
"aa_length": 1000,
"cds_start": 2984,
"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": "C",
"aa_alt": "Y",
"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.2951G>A",
"hgvs_p": "p.Cys984Tyr",
"transcript": "ENST00000877491.1",
"protein_id": "ENSP00000547550.1",
"transcript_support_level": null,
"aa_start": 984,
"aa_end": null,
"aa_length": 989,
"cds_start": 2951,
"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": "C",
"aa_alt": "Y",
"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.2894G>A",
"hgvs_p": "p.Cys965Tyr",
"transcript": "ENST00000965341.1",
"protein_id": "ENSP00000635400.1",
"transcript_support_level": null,
"aa_start": 965,
"aa_end": null,
"aa_length": 970,
"cds_start": 2894,
"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": "C",
"aa_alt": "Y",
"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.2885G>A",
"hgvs_p": "p.Cys962Tyr",
"transcript": "ENST00000911611.1",
"protein_id": "ENSP00000581670.1",
"transcript_support_level": null,
"aa_start": 962,
"aa_end": null,
"aa_length": 967,
"cds_start": 2885,
"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": "C",
"aa_alt": "Y",
"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.2870G>A",
"hgvs_p": "p.Cys957Tyr",
"transcript": "ENST00000911612.1",
"protein_id": "ENSP00000581671.1",
"transcript_support_level": null,
"aa_start": 957,
"aa_end": null,
"aa_length": 962,
"cds_start": 2870,
"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": "C",
"aa_alt": "Y",
"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.2870G>A",
"hgvs_p": "p.Cys957Tyr",
"transcript": "ENST00000965324.1",
"protein_id": "ENSP00000635383.1",
"transcript_support_level": null,
"aa_start": 957,
"aa_end": null,
"aa_length": 962,
"cds_start": 2870,
"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": "C",
"aa_alt": "Y",
"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.2867G>A",
"hgvs_p": "p.Cys956Tyr",
"transcript": "ENST00000877475.1",
"protein_id": "ENSP00000547534.1",
"transcript_support_level": null,
"aa_start": 956,
"aa_end": null,
"aa_length": 961,
"cds_start": 2867,
"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": "C",
"aa_alt": "Y",
"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.2840G>A",
"hgvs_p": "p.Cys947Tyr",
"transcript": "ENST00000877488.1",
"protein_id": "ENSP00000547547.1",
"transcript_support_level": null,
"aa_start": 947,
"aa_end": null,
"aa_length": 952,
"cds_start": 2840,
"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": "C",
"aa_alt": "Y",
"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.2831G>A",
"hgvs_p": "p.Cys944Tyr",
"transcript": "ENST00000965327.1",
"protein_id": "ENSP00000635386.1",
"transcript_support_level": null,
"aa_start": 944,
"aa_end": null,
"aa_length": 949,
"cds_start": 2831,
"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": "C",
"aa_alt": "Y",
"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.2819G>A",
"hgvs_p": "p.Cys940Tyr",
"transcript": "ENST00000877477.1",
"protein_id": "ENSP00000547536.1",
"transcript_support_level": null,
"aa_start": 940,
"aa_end": null,
"aa_length": 945,
"cds_start": 2819,
"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": "C",
"aa_alt": "Y",
"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.2804G>A",
"hgvs_p": "p.Cys935Tyr",
"transcript": "ENST00000965330.1",
"protein_id": "ENSP00000635389.1",
"transcript_support_level": null,
"aa_start": 935,
"aa_end": null,
"aa_length": 940,
"cds_start": 2804,
"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": "C",
"aa_alt": "Y",
"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.2759G>A",
"hgvs_p": "p.Cys920Tyr",
"transcript": "ENST00000877480.1",
"protein_id": "ENSP00000547539.1",
"transcript_support_level": null,
"aa_start": 920,
"aa_end": null,
"aa_length": 925,
"cds_start": 2759,
"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": "C",
"aa_alt": "Y",
"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.2732G>A",
"hgvs_p": "p.Cys911Tyr",
"transcript": "NM_199443.3",
"protein_id": "NP_955475.1",
"transcript_support_level": null,
"aa_start": 911,
"aa_end": null,
"aa_length": 916,
"cds_start": 2732,
"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": "C",
"aa_alt": "Y",
"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.2729G>A",
"hgvs_p": "p.Cys910Tyr",
"transcript": "ENST00000877484.1",
"protein_id": "ENSP00000547543.1",
"transcript_support_level": null,
"aa_start": 910,
"aa_end": null,
"aa_length": 915,
"cds_start": 2729,
"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": "C",
"aa_alt": "Y",
"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.2726G>A",
"hgvs_p": "p.Cys909Tyr",
"transcript": "ENST00000877485.1",
"protein_id": "ENSP00000547544.1",
"transcript_support_level": null,
"aa_start": 909,
"aa_end": null,
"aa_length": 914,
"cds_start": 2726,
"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": "C",
"aa_alt": "Y",
"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.2714G>A",
"hgvs_p": "p.Cys905Tyr",
"transcript": "ENST00000877473.1",
"protein_id": "ENSP00000547532.1",
"transcript_support_level": null,
"aa_start": 905,
"aa_end": null,
"aa_length": 910,
"cds_start": 2714,
"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": "C",
"aa_alt": "Y",
"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.2699G>A",
"hgvs_p": "p.Cys900Tyr",
"transcript": "ENST00000877492.1",
"protein_id": "ENSP00000547551.1",
"transcript_support_level": null,
"aa_start": 900,
"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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"biotype": "retained_intron",
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{
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"strand": false,
"consequences": [
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],
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"gene_symbol": "USP4",
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"biotype": "retained_intron",
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],
"gene_symbol": "USP4",
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"dbsnp": "rs1381177742",
"frequency_reference_population": 0.000006573412,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": 0.00000657341,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06438189744949341,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.016,
"revel_prediction": "Benign",
"alphamissense_score": 0.0849,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.472,
"phylop100way_prediction": "Benign",
"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": -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": "NM_003363.4",
"gene_symbol": "USP4",
"hgnc_id": 12627,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2873G>A",
"hgvs_p": "p.Cys958Tyr"
}
],
"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
}