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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: 3-119447073-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=119447073&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 119447073,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_018266.3",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "NM_018266.3",
"protein_id": "NP_060736.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 488,
"cds_start": 520,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000319172.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018266.3"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "ENST00000319172.10",
"protein_id": "ENSP00000326063.5",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 488,
"cds_start": 520,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018266.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000319172.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "n.*188C>G",
"hgvs_p": null,
"transcript": "ENST00000438581.6",
"protein_id": "ENSP00000402149.2",
"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": "nonsense_mediated_decay",
"feature": "ENST00000438581.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "n.*188C>G",
"hgvs_p": null,
"transcript": "ENST00000438581.6",
"protein_id": "ENSP00000402149.2",
"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": "nonsense_mediated_decay",
"feature": "ENST00000438581.6"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.643C>G",
"hgvs_p": "p.Leu215Val",
"transcript": "ENST00000924820.1",
"protein_id": "ENSP00000594879.1",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 529,
"cds_start": 643,
"cds_end": null,
"cds_length": 1590,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924820.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "ENST00000955954.1",
"protein_id": "ENSP00000626013.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 501,
"cds_start": 520,
"cds_end": null,
"cds_length": 1506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955954.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "ENST00000884856.1",
"protein_id": "ENSP00000554915.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 488,
"cds_start": 520,
"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": "ENST00000884856.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "ENST00000884857.1",
"protein_id": "ENSP00000554916.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 488,
"cds_start": 520,
"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": "ENST00000884857.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "ENST00000884859.1",
"protein_id": "ENSP00000554918.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 488,
"cds_start": 520,
"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": "ENST00000884859.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "ENST00000924822.1",
"protein_id": "ENSP00000594881.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 488,
"cds_start": 520,
"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": "ENST00000924822.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "ENST00000955955.1",
"protein_id": "ENSP00000626014.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 488,
"cds_start": 520,
"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": "ENST00000955955.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.511C>G",
"hgvs_p": "p.Leu171Val",
"transcript": "ENST00000924823.1",
"protein_id": "ENSP00000594882.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 485,
"cds_start": 511,
"cds_end": null,
"cds_length": 1458,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924823.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.436C>G",
"hgvs_p": "p.Leu146Val",
"transcript": "ENST00000884858.1",
"protein_id": "ENSP00000554917.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 460,
"cds_start": 436,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884858.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.436C>G",
"hgvs_p": "p.Leu146Val",
"transcript": "ENST00000884860.1",
"protein_id": "ENSP00000554919.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 460,
"cds_start": 436,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884860.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.436C>G",
"hgvs_p": "p.Leu146Val",
"transcript": "ENST00000924821.1",
"protein_id": "ENSP00000594880.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 460,
"cds_start": 436,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924821.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.436C>G",
"hgvs_p": "p.Leu146Val",
"transcript": "ENST00000955953.1",
"protein_id": "ENSP00000626012.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 460,
"cds_start": 436,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955953.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"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": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "ENST00000468676.5",
"protein_id": "ENSP00000418796.1",
"transcript_support_level": 3,
"aa_start": 174,
"aa_end": null,
"aa_length": 190,
"cds_start": 520,
"cds_end": null,
"cds_length": 575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000468676.5"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "XM_006713687.3",
"protein_id": "XP_006713750.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 488,
"cds_start": 520,
"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": "XM_006713687.3"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.436C>G",
"hgvs_p": "p.Leu146Val",
"transcript": "XM_017006788.3",
"protein_id": "XP_016862277.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 460,
"cds_start": 436,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006788.3"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.436C>G",
"hgvs_p": "p.Leu146Val",
"transcript": "XM_047448511.1",
"protein_id": "XP_047304467.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 460,
"cds_start": 436,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448511.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "XM_005247578.3",
"protein_id": "XP_005247635.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 377,
"cds_start": 520,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005247578.3"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM39A",
"gene_hgnc_id": 25600,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "XM_047448512.1",
"protein_id": "XP_047304468.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 377,
"cds_start": 520,
"cds_end": null,
"cds_length": 1134,
"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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],
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{
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],
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{
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],
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"gene_symbol": "TMEM39A",
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"transcript": "ENST00000486159.5",
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"biotype": "pseudogene",
"feature": "ENST00000486159.5"
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],
"gene_symbol": "TMEM39A",
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"dbsnp": "rs367905542",
"frequency_reference_population": 0.00006815357,
"hom_count_reference_population": 0,
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"gnomad_exomes_ac": 102,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.22680720686912537,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.168,
"revel_prediction": "Benign",
"alphamissense_score": 0.288,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.042,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018266.3",
"gene_symbol": "TMEM39A",
"hgnc_id": 25600,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val"
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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
}