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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: 3-15258897-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=15258897&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 15258897,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004844.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.823G>A",
"hgvs_p": "p.Ala275Thr",
"transcript": "NM_004844.5",
"protein_id": "NP_004835.2",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 455,
"cds_start": 823,
"cds_end": null,
"cds_length": 1368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000383791.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004844.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.823G>A",
"hgvs_p": "p.Ala275Thr",
"transcript": "ENST00000383791.8",
"protein_id": "ENSP00000373301.3",
"transcript_support_level": 1,
"aa_start": 275,
"aa_end": null,
"aa_length": 455,
"cds_start": 823,
"cds_end": null,
"cds_length": 1368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004844.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000383791.8"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.352G>A",
"hgvs_p": "p.Ala118Thr",
"transcript": "ENST00000408919.7",
"protein_id": "ENSP00000386231.3",
"transcript_support_level": 1,
"aa_start": 118,
"aa_end": null,
"aa_length": 298,
"cds_start": 352,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000408919.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5-AS1",
"gene_hgnc_id": 44501,
"hgvs_c": "n.3687C>T",
"hgvs_p": null,
"transcript": "ENST00000420195.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000420195.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.883G>A",
"hgvs_p": "p.Ala295Thr",
"transcript": "ENST00000947043.1",
"protein_id": "ENSP00000617102.1",
"transcript_support_level": null,
"aa_start": 295,
"aa_end": null,
"aa_length": 475,
"cds_start": 883,
"cds_end": null,
"cds_length": 1428,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947043.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.823G>A",
"hgvs_p": "p.Ala275Thr",
"transcript": "ENST00000947042.1",
"protein_id": "ENSP00000617101.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 454,
"cds_start": 823,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947042.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.793G>A",
"hgvs_p": "p.Ala265Thr",
"transcript": "ENST00000885923.1",
"protein_id": "ENSP00000555982.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 445,
"cds_start": 793,
"cds_end": null,
"cds_length": 1338,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885923.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.664G>A",
"hgvs_p": "p.Ala222Thr",
"transcript": "ENST00000885925.1",
"protein_id": "ENSP00000555984.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 402,
"cds_start": 664,
"cds_end": null,
"cds_length": 1209,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885925.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.658G>A",
"hgvs_p": "p.Ala220Thr",
"transcript": "ENST00000885926.1",
"protein_id": "ENSP00000555985.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 400,
"cds_start": 658,
"cds_end": null,
"cds_length": 1203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885926.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.658G>A",
"hgvs_p": "p.Ala220Thr",
"transcript": "ENST00000947046.1",
"protein_id": "ENSP00000617105.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 399,
"cds_start": 658,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947046.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.649G>A",
"hgvs_p": "p.Ala217Thr",
"transcript": "ENST00000947045.1",
"protein_id": "ENSP00000617104.1",
"transcript_support_level": null,
"aa_start": 217,
"aa_end": null,
"aa_length": 397,
"cds_start": 649,
"cds_end": null,
"cds_length": 1194,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947045.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.823G>A",
"hgvs_p": "p.Ala275Thr",
"transcript": "ENST00000885924.1",
"protein_id": "ENSP00000555983.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 368,
"cds_start": 823,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885924.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.793G>A",
"hgvs_p": "p.Ala265Thr",
"transcript": "ENST00000885927.1",
"protein_id": "ENSP00000555986.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 358,
"cds_start": 793,
"cds_end": null,
"cds_length": 1077,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885927.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.529G>A",
"hgvs_p": "p.Ala177Thr",
"transcript": "ENST00000947044.1",
"protein_id": "ENSP00000617103.1",
"transcript_support_level": null,
"aa_start": 177,
"aa_end": null,
"aa_length": 357,
"cds_start": 529,
"cds_end": null,
"cds_length": 1074,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947044.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.658G>A",
"hgvs_p": "p.Ala220Thr",
"transcript": "ENST00000885928.1",
"protein_id": "ENSP00000555987.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 313,
"cds_start": 658,
"cds_end": null,
"cds_length": 942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885928.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.352G>A",
"hgvs_p": "p.Ala118Thr",
"transcript": "NM_001018009.4",
"protein_id": "NP_001018009.2",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 298,
"cds_start": 352,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001018009.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.352G>A",
"hgvs_p": "p.Ala118Thr",
"transcript": "ENST00000426925.5",
"protein_id": "ENSP00000388553.1",
"transcript_support_level": 2,
"aa_start": 118,
"aa_end": null,
"aa_length": 298,
"cds_start": 352,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000426925.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.352G>A",
"hgvs_p": "p.Ala118Thr",
"transcript": "ENST00000366391.6",
"protein_id": "ENSP00000394115.1",
"transcript_support_level": 3,
"aa_start": 118,
"aa_end": null,
"aa_length": 127,
"cds_start": 352,
"cds_end": null,
"cds_length": 384,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000366391.6"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.802G>A",
"hgvs_p": "p.Ala268Thr",
"transcript": "XM_017007525.2",
"protein_id": "XP_016863014.2",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 448,
"cds_start": 802,
"cds_end": null,
"cds_length": 1347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017007525.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.784G>A",
"hgvs_p": "p.Ala262Thr",
"transcript": "XM_047449240.1",
"protein_id": "XP_047305196.1",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 442,
"cds_start": 784,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449240.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.703G>A",
"hgvs_p": "p.Ala235Thr",
"transcript": "XM_011534251.3",
"protein_id": "XP_011532553.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 415,
"cds_start": 703,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011534251.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5",
"gene_hgnc_id": 10827,
"hgvs_c": "c.823G>A",
"hgvs_p": "p.Ala275Thr",
"transcript": "XM_047449241.1",
"protein_id": "XP_047305197.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 368,
"cds_start": 823,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
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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": "nonsense_mediated_decay",
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],
"gene_symbol": "SH3BP5",
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"dbsnp": "rs768845465",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 38,
"gnomad_exomes_af": 0.0000253098,
"gnomad_genomes_af": 0.0000065684,
"gnomad_exomes_ac": 37,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3294364809989929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.358,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5114,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.785,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004844.5",
"gene_symbol": "SH3BP5",
"hgnc_id": 10827,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.823G>A",
"hgvs_p": "p.Ala275Thr"
},
{
"score": 1,
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"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000420195.1",
"gene_symbol": "SH3BP5-AS1",
"hgnc_id": 44501,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.3687C>T",
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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
}