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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: 3-141292303-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=141292303&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 141292303,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_152282.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "NM_001037172.3",
"protein_id": "NP_001032249.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000286353.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001037172.3"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000286353.9",
"protein_id": "ENSP00000286353.4",
"transcript_support_level": 1,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001037172.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000286353.9"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000393010.6",
"protein_id": "ENSP00000376733.2",
"transcript_support_level": 1,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000393010.6"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.514A>T",
"hgvs_p": "p.Arg172Trp",
"transcript": "ENST00000508812.1",
"protein_id": "ENSP00000422901.1",
"transcript_support_level": 1,
"aa_start": 172,
"aa_end": null,
"aa_length": 471,
"cds_start": 514,
"cds_end": null,
"cds_length": 1416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000508812.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "NM_152282.5",
"protein_id": "NP_689495.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152282.5"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000879101.1",
"protein_id": "ENSP00000549160.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879101.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000879102.1",
"protein_id": "ENSP00000549161.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879102.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000879104.1",
"protein_id": "ENSP00000549163.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879104.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000925230.1",
"protein_id": "ENSP00000595289.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925230.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000925231.1",
"protein_id": "ENSP00000595290.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925231.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000925232.1",
"protein_id": "ENSP00000595291.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925232.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000971913.1",
"protein_id": "ENSP00000641972.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971913.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000971914.1",
"protein_id": "ENSP00000641973.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971914.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000971915.1",
"protein_id": "ENSP00000641974.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971915.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000971916.1",
"protein_id": "ENSP00000641975.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971916.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000971917.1",
"protein_id": "ENSP00000641976.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971917.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000971918.1",
"protein_id": "ENSP00000641977.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971918.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp",
"transcript": "ENST00000971919.1",
"protein_id": "ENSP00000641978.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 480,
"cds_start": 541,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971919.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.490A>T",
"hgvs_p": "p.Arg164Trp",
"transcript": "ENST00000504264.5",
"protein_id": "ENSP00000426877.1",
"transcript_support_level": 2,
"aa_start": 164,
"aa_end": null,
"aa_length": 463,
"cds_start": 490,
"cds_end": null,
"cds_length": 1392,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000504264.5"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.427A>T",
"hgvs_p": "p.Arg143Trp",
"transcript": "NM_001282728.2",
"protein_id": "NP_001269657.1",
"transcript_support_level": null,
"aa_start": 143,
"aa_end": null,
"aa_length": 442,
"cds_start": 427,
"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": "NM_001282728.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.427A>T",
"hgvs_p": "p.Arg143Trp",
"transcript": "ENST00000502783.5",
"protein_id": "ENSP00000422558.1",
"transcript_support_level": 2,
"aa_start": 143,
"aa_end": null,
"aa_length": 442,
"cds_start": 427,
"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": "ENST00000502783.5"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXYLP1",
"gene_hgnc_id": 26303,
"hgvs_c": "c.382A>T",
"hgvs_p": "p.Arg128Trp",
"transcript": "ENST00000879103.1",
"protein_id": "ENSP00000549162.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 427,
"cds_start": 382,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
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{
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},
{
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{
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"consequences": [
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],
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"feature": "ENST00000514263.2"
},
{
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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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"transcript": "ENST00000637751.1",
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],
"gene_symbol": "PXYLP1",
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"dbsnp": null,
"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": 0.9715255498886108,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.74,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1545,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.356,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_152282.5",
"gene_symbol": "PXYLP1",
"hgnc_id": 26303,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.541A>T",
"hgvs_p": "p.Arg181Trp"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000507698.1",
"gene_symbol": "ENSG00000249417",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.167-24695T>A",
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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
}