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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: 3-193647127-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=193647127&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 193647127,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000361510.8",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1817G>A",
"hgvs_p": "p.Cys606Tyr",
"transcript": "NM_130837.3",
"protein_id": "NP_570850.2",
"transcript_support_level": null,
"aa_start": 606,
"aa_end": null,
"aa_length": 1015,
"cds_start": 1817,
"cds_end": null,
"cds_length": 3048,
"cdna_start": 1987,
"cdna_end": null,
"cdna_length": 6429,
"mane_select": "ENST00000361510.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1817G>A",
"hgvs_p": "p.Cys606Tyr",
"transcript": "ENST00000361510.8",
"protein_id": "ENSP00000355324.2",
"transcript_support_level": 5,
"aa_start": 606,
"aa_end": null,
"aa_length": 1015,
"cds_start": 1817,
"cds_end": null,
"cds_length": 3048,
"cdna_start": 1987,
"cdna_end": null,
"cdna_length": 6429,
"mane_select": "NM_130837.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1763G>A",
"hgvs_p": "p.Cys588Tyr",
"transcript": "ENST00000361908.8",
"protein_id": "ENSP00000354681.3",
"transcript_support_level": 1,
"aa_start": 588,
"aa_end": null,
"aa_length": 997,
"cds_start": 1763,
"cds_end": null,
"cds_length": 2994,
"cdna_start": 1955,
"cdna_end": null,
"cdna_length": 6397,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1763G>A",
"hgvs_p": "p.Cys588Tyr",
"transcript": "NM_130836.3",
"protein_id": "NP_570849.2",
"transcript_support_level": null,
"aa_start": 588,
"aa_end": null,
"aa_length": 997,
"cds_start": 1763,
"cds_end": null,
"cds_length": 2994,
"cdna_start": 1933,
"cdna_end": null,
"cdna_length": 6375,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1709G>A",
"hgvs_p": "p.Cys570Tyr",
"transcript": "NM_130835.3",
"protein_id": "NP_570848.1",
"transcript_support_level": null,
"aa_start": 570,
"aa_end": null,
"aa_length": 979,
"cds_start": 1709,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 1879,
"cdna_end": null,
"cdna_length": 6321,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1709G>A",
"hgvs_p": "p.Cys570Tyr",
"transcript": "ENST00000361715.6",
"protein_id": "ENSP00000355311.2",
"transcript_support_level": 5,
"aa_start": 570,
"aa_end": null,
"aa_length": 979,
"cds_start": 1709,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 1943,
"cdna_end": null,
"cdna_length": 6384,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1706G>A",
"hgvs_p": "p.Cys569Tyr",
"transcript": "NM_130834.3",
"protein_id": "NP_570847.2",
"transcript_support_level": null,
"aa_start": 569,
"aa_end": null,
"aa_length": 978,
"cds_start": 1706,
"cds_end": null,
"cds_length": 2937,
"cdna_start": 1876,
"cdna_end": null,
"cdna_length": 6318,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1706G>A",
"hgvs_p": "p.Cys569Tyr",
"transcript": "ENST00000392437.6",
"protein_id": "ENSP00000376232.2",
"transcript_support_level": 3,
"aa_start": 569,
"aa_end": null,
"aa_length": 978,
"cds_start": 1706,
"cds_end": null,
"cds_length": 2937,
"cdna_start": 1804,
"cdna_end": null,
"cdna_length": 4087,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1652G>A",
"hgvs_p": "p.Cys551Tyr",
"transcript": "ENST00000392436.7",
"protein_id": "ENSP00000376231.3",
"transcript_support_level": 3,
"aa_start": 551,
"aa_end": null,
"aa_length": 972,
"cds_start": 1652,
"cds_end": null,
"cds_length": 2919,
"cdna_start": 1810,
"cdna_end": null,
"cdna_length": 3579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1667G>A",
"hgvs_p": "p.Cys556Tyr",
"transcript": "ENST00000645553.1",
"protein_id": "ENSP00000494725.1",
"transcript_support_level": null,
"aa_start": 556,
"aa_end": null,
"aa_length": 965,
"cds_start": 1667,
"cds_end": null,
"cds_length": 2898,
"cdna_start": 1758,
"cdna_end": null,
"cdna_length": 5008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1655G>A",
"hgvs_p": "p.Cys552Tyr",
"transcript": "NM_130833.3",
"protein_id": "NP_570846.1",
"transcript_support_level": null,
"aa_start": 552,
"aa_end": null,
"aa_length": 961,
"cds_start": 1655,
"cds_end": null,
"cds_length": 2886,
"cdna_start": 1825,
"cdna_end": null,
"cdna_length": 6267,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1655G>A",
"hgvs_p": "p.Cys552Tyr",
"transcript": "ENST00000361150.6",
"protein_id": "ENSP00000354781.2",
"transcript_support_level": 5,
"aa_start": 552,
"aa_end": null,
"aa_length": 961,
"cds_start": 1655,
"cds_end": null,
"cds_length": 2886,
"cdna_start": 1889,
"cdna_end": null,
"cdna_length": 6330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1652G>A",
"hgvs_p": "p.Cys551Tyr",
"transcript": "NM_015560.3",
"protein_id": "NP_056375.2",
"transcript_support_level": null,
"aa_start": 551,
"aa_end": null,
"aa_length": 960,
"cds_start": 1652,
"cds_end": null,
"cds_length": 2883,
"cdna_start": 1822,
"cdna_end": null,
"cdna_length": 6264,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1652G>A",
"hgvs_p": "p.Cys551Tyr",
"transcript": "ENST00000361828.7",
"protein_id": "ENSP00000354429.3",
"transcript_support_level": 5,
"aa_start": 551,
"aa_end": null,
"aa_length": 960,
"cds_start": 1652,
"cds_end": null,
"cds_length": 2883,
"cdna_start": 1886,
"cdna_end": null,
"cdna_length": 6328,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1598G>A",
"hgvs_p": "p.Cys533Tyr",
"transcript": "NM_130832.3",
"protein_id": "NP_570845.1",
"transcript_support_level": null,
"aa_start": 533,
"aa_end": null,
"aa_length": 942,
"cds_start": 1598,
"cds_end": null,
"cds_length": 2829,
"cdna_start": 1768,
"cdna_end": null,
"cdna_length": 6210,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1544G>A",
"hgvs_p": "p.Cys515Tyr",
"transcript": "NM_130831.3",
"protein_id": "NP_570844.1",
"transcript_support_level": null,
"aa_start": 515,
"aa_end": null,
"aa_length": 924,
"cds_start": 1544,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 1714,
"cdna_end": null,
"cdna_length": 6156,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1544G>A",
"hgvs_p": "p.Cys515Tyr",
"transcript": "ENST00000646793.1",
"protein_id": "ENSP00000494512.1",
"transcript_support_level": null,
"aa_start": 515,
"aa_end": null,
"aa_length": 924,
"cds_start": 1544,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 1675,
"cdna_end": null,
"cdna_length": 5830,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1334G>A",
"hgvs_p": "p.Cys445Tyr",
"transcript": "ENST00000643329.1",
"protein_id": "ENSP00000493673.1",
"transcript_support_level": null,
"aa_start": 445,
"aa_end": null,
"aa_length": 854,
"cds_start": 1334,
"cds_end": null,
"cds_length": 2565,
"cdna_start": 1914,
"cdna_end": null,
"cdna_length": 6068,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1283G>A",
"hgvs_p": "p.Cys428Tyr",
"transcript": "NM_001354663.2",
"protein_id": "NP_001341592.1",
"transcript_support_level": null,
"aa_start": 428,
"aa_end": null,
"aa_length": 837,
"cds_start": 1283,
"cds_end": null,
"cds_length": 2514,
"cdna_start": 1883,
"cdna_end": null,
"cdna_length": 6325,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1280G>A",
"hgvs_p": "p.Cys427Tyr",
"transcript": "NM_001354664.2",
"protein_id": "NP_001341593.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 836,
"cds_start": 1280,
"cds_end": null,
"cds_length": 2511,
"cdna_start": 1880,
"cdna_end": null,
"cdna_length": 6322,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.638G>A",
"hgvs_p": "p.Cys213Tyr",
"transcript": "ENST00000646544.1",
"protein_id": "ENSP00000495028.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 622,
"cds_start": 638,
"cds_end": null,
"cds_length": 1869,
"cdna_start": 640,
"cdna_end": null,
"cdna_length": 5071,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1817G>A",
"hgvs_p": "p.Cys606Tyr",
"transcript": "XM_047448206.1",
"protein_id": "XP_047304162.1",
"transcript_support_level": null,
"aa_start": 606,
"aa_end": null,
"aa_length": 1047,
"cds_start": 1817,
"cds_end": null,
"cds_length": 3144,
"cdna_start": 1987,
"cdna_end": null,
"cdna_length": 3338,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
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},
{
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],
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"exon_count": 5,
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"gene_symbol": "ENSG00000306963",
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},
{
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}
],
"gene_symbol": "OPA1",
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"dbsnp": "rs879255592",
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"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,
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"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9050506949424744,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.867,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9256,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.51,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 10.003,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
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"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
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"acmg_score": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM1",
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000361510.8",
"gene_symbol": "OPA1",
"hgnc_id": 8140,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.1817G>A",
"hgvs_p": "p.Cys606Tyr"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000822231.1",
"gene_symbol": "ENSG00000306963",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.474C>T",
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},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "XR_924835.3",
"gene_symbol": "LOC102724808",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*128C>T",
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}
],
"clinvar_disease": " and neuropathy, ataxia, myopathy, ophthalmoplegia,Optic atrophy with or without deafness",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Optic atrophy with or without deafness, ophthalmoplegia, myopathy, ataxia, and neuropathy",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}