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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: 3-179875406-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=179875406&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 179875406,
"ref": "T",
"alt": "C",
"effect": "start_lost",
"transcript": "NM_001256756.2",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Met193Val",
"transcript": "NM_016559.3",
"protein_id": "NP_057643.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 626,
"cds_start": 577,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 915,
"cdna_end": null,
"cdna_length": 9089,
"mane_select": "ENST00000467460.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016559.3"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Met193Val",
"transcript": "ENST00000467460.6",
"protein_id": "ENSP00000419975.1",
"transcript_support_level": 1,
"aa_start": 193,
"aa_end": null,
"aa_length": 626,
"cds_start": 577,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 915,
"cdna_end": null,
"cdna_length": 9089,
"mane_select": "NM_016559.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000467460.6"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.571A>G",
"hgvs_p": "p.Met191Val",
"transcript": "ENST00000263962.12",
"protein_id": "ENSP00000263962.8",
"transcript_support_level": 1,
"aa_start": 191,
"aa_end": null,
"aa_length": 624,
"cds_start": 571,
"cds_end": null,
"cds_length": 1875,
"cdna_start": 742,
"cdna_end": null,
"cdna_length": 2818,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263962.12"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Met158Val",
"transcript": "ENST00000485199.5",
"protein_id": "ENSP00000418440.1",
"transcript_support_level": 1,
"aa_start": 158,
"aa_end": null,
"aa_length": 591,
"cds_start": 472,
"cds_end": null,
"cds_length": 1776,
"cdna_start": 926,
"cdna_end": null,
"cdna_length": 2992,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000485199.5"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_001256756.2",
"protein_id": "NP_001243685.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 434,
"cds_start": 1,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 661,
"cdna_end": null,
"cdna_length": 8835,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001256756.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_001349399.2",
"protein_id": "NP_001336328.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 434,
"cds_start": 1,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 731,
"cdna_end": null,
"cdna_length": 8905,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349399.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_001349401.2",
"protein_id": "NP_001336330.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 434,
"cds_start": 1,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 626,
"cdna_end": null,
"cdna_length": 8800,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349401.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_001349404.2",
"protein_id": "NP_001336333.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 434,
"cds_start": 1,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 431,
"cdna_end": null,
"cdna_length": 8605,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349404.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_001349406.2",
"protein_id": "NP_001336335.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 434,
"cds_start": 1,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 709,
"cdna_end": null,
"cdna_length": 8883,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349406.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_001349408.2",
"protein_id": "NP_001336337.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 434,
"cds_start": 1,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 814,
"cdna_end": null,
"cdna_length": 8988,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349408.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_001349409.2",
"protein_id": "NP_001336338.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 434,
"cds_start": 1,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 654,
"cdna_end": null,
"cdna_length": 8828,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349409.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_001349410.2",
"protein_id": "NP_001336339.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 434,
"cds_start": 1,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 466,
"cdna_end": null,
"cdna_length": 8640,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349410.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000468741.5",
"protein_id": "ENSP00000418665.1",
"transcript_support_level": 2,
"aa_start": 1,
"aa_end": null,
"aa_length": 434,
"cds_start": 1,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 695,
"cdna_end": null,
"cdna_length": 2309,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000468741.5"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000496721.5",
"protein_id": "ENSP00000418746.1",
"transcript_support_level": 3,
"aa_start": 1,
"aa_end": null,
"aa_length": 69,
"cds_start": 1,
"cds_end": null,
"cds_length": 211,
"cdna_start": 262,
"cdna_end": null,
"cdna_length": 472,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000496721.5"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000491640.5",
"protein_id": "ENSP00000419790.1",
"transcript_support_level": 4,
"aa_start": 1,
"aa_end": null,
"aa_length": 33,
"cds_start": 1,
"cds_end": null,
"cds_length": 104,
"cdna_start": 460,
"cdna_end": null,
"cdna_length": 563,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000491640.5"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_011512891.3",
"protein_id": "XP_011511193.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 434,
"cds_start": 1,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 1218,
"cdna_end": null,
"cdna_length": 9392,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512891.3"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.742A>G",
"hgvs_p": "p.Met248Val",
"transcript": "NM_001349386.2",
"protein_id": "NP_001336315.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 681,
"cds_start": 742,
"cds_end": null,
"cds_length": 2046,
"cdna_start": 930,
"cdna_end": null,
"cdna_length": 9104,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349386.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.649A>G",
"hgvs_p": "p.Met217Val",
"transcript": "NM_001349387.2",
"protein_id": "NP_001336316.1",
"transcript_support_level": null,
"aa_start": 217,
"aa_end": null,
"aa_length": 650,
"cds_start": 649,
"cds_end": null,
"cds_length": 1953,
"cdna_start": 926,
"cdna_end": null,
"cdna_length": 9100,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349387.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.649A>G",
"hgvs_p": "p.Met217Val",
"transcript": "NM_001349388.2",
"protein_id": "NP_001336317.1",
"transcript_support_level": null,
"aa_start": 217,
"aa_end": null,
"aa_length": 650,
"cds_start": 649,
"cds_end": null,
"cds_length": 1953,
"cdna_start": 1623,
"cdna_end": null,
"cdna_length": 9797,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349388.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.643A>G",
"hgvs_p": "p.Met215Val",
"transcript": "NM_001349389.2",
"protein_id": "NP_001336318.1",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 648,
"cds_start": 643,
"cds_end": null,
"cds_length": 1947,
"cdna_start": 981,
"cdna_end": null,
"cdna_length": 9155,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349389.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.637A>G",
"hgvs_p": "p.Met213Val",
"transcript": "NM_001349390.2",
"protein_id": "NP_001336319.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 646,
"cds_start": 637,
"cds_end": null,
"cds_length": 1941,
"cdna_start": 825,
"cdna_end": null,
"cdna_length": 8999,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349390.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX5L",
"gene_hgnc_id": 30024,
"hgvs_c": "c.571A>G",
"hgvs_p": "p.Met191Val",
"transcript": "NM_001256750.2",
"protein_id": "NP_001243679.1",
"transcript_support_level": null,
"aa_start": 191,
"aa_end": null,
"aa_length": 624,
"cds_start": 571,
"cds_end": null,
"cds_length": 1875,
"cdna_start": 909,
"cdna_end": null,
"cdna_length": 9083,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001256750.2"
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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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"transcript": "NR_146167.2",
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"feature": "NR_146167.2"
},
{
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"consequences": [
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],
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"gene_symbol": "PEX5L",
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"transcript": "ENST00000463761.1",
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"biotype": "protein_coding",
"feature": "ENST00000463761.1"
}
],
"gene_symbol": "PEX5L",
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"dbsnp": "rs1468030868",
"frequency_reference_population": 6.845133e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84513e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.17501521110534668,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.216,
"revel_prediction": "Benign",
"alphamissense_score": 0.0522,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.062,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Supporting,PM2",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PVS1_Supporting",
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001256756.2",
"gene_symbol": "PEX5L",
"hgnc_id": 30024,
"effects": [
"start_lost"
],
"inheritance_mode": "",
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?"
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{
"score": 0,
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"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000466064.1",
"gene_symbol": "PEX5L-AS1",
"hgnc_id": 41251,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.31T>C",
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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
}