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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: 10-93758208-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=93758208&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 93758208,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_005097.4",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile",
"transcript": "NM_005097.4",
"protein_id": "NP_005088.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 557,
"cds_start": 64,
"cds_end": null,
"cds_length": 1674,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 2239,
"mane_select": "ENST00000371418.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile",
"transcript": "ENST00000371418.9",
"protein_id": "ENSP00000360472.4",
"transcript_support_level": 1,
"aa_start": 22,
"aa_end": null,
"aa_length": 557,
"cds_start": 64,
"cds_end": null,
"cds_length": 1674,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 2239,
"mane_select": "NM_005097.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile",
"transcript": "ENST00000371413.4",
"protein_id": "ENSP00000360467.3",
"transcript_support_level": 1,
"aa_start": 22,
"aa_end": null,
"aa_length": 291,
"cds_start": 64,
"cds_end": null,
"cds_length": 876,
"cdna_start": 64,
"cdna_end": null,
"cdna_length": 1247,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "n.64T>A",
"hgvs_p": null,
"transcript": "ENST00000627420.2",
"protein_id": "ENSP00000487116.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2278,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile",
"transcript": "ENST00000629035.2",
"protein_id": "ENSP00000486908.1",
"transcript_support_level": 5,
"aa_start": 22,
"aa_end": null,
"aa_length": 533,
"cds_start": 64,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 358,
"cdna_end": null,
"cdna_length": 2251,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile",
"transcript": "NM_001308276.2",
"protein_id": "NP_001295205.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 509,
"cds_start": 64,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 2095,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile",
"transcript": "ENST00000630047.2",
"protein_id": "ENSP00000485917.1",
"transcript_support_level": 2,
"aa_start": 22,
"aa_end": null,
"aa_length": 509,
"cds_start": 64,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 238,
"cdna_end": null,
"cdna_length": 1751,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile",
"transcript": "NM_001308275.2",
"protein_id": "NP_001295204.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 291,
"cds_start": 64,
"cds_end": null,
"cds_length": 876,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 1458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile",
"transcript": "ENST00000636155.1",
"protein_id": "ENSP00000490355.1",
"transcript_support_level": 5,
"aa_start": 22,
"aa_end": null,
"aa_length": 287,
"cds_start": 64,
"cds_end": null,
"cds_length": 864,
"cdna_start": 181,
"cdna_end": null,
"cdna_length": 1618,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile",
"transcript": "ENST00000630184.2",
"protein_id": "ENSP00000486607.1",
"transcript_support_level": 2,
"aa_start": 22,
"aa_end": null,
"aa_length": 168,
"cds_start": 64,
"cds_end": null,
"cds_length": 507,
"cdna_start": 271,
"cdna_end": null,
"cdna_length": 2936,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile",
"transcript": "ENST00000478763.2",
"protein_id": "ENSP00000486517.1",
"transcript_support_level": 2,
"aa_start": 22,
"aa_end": null,
"aa_length": 96,
"cds_start": 64,
"cds_end": null,
"cds_length": 291,
"cdna_start": 296,
"cdna_end": null,
"cdna_length": 600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile",
"transcript": "ENST00000627699.1",
"protein_id": "ENSP00000485868.1",
"transcript_support_level": 3,
"aa_start": 22,
"aa_end": null,
"aa_length": 72,
"cds_start": 64,
"cds_end": null,
"cds_length": 219,
"cdna_start": 133,
"cdna_end": null,
"cdna_length": 664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile",
"transcript": "XM_017016911.3",
"protein_id": "XP_016872400.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 281,
"cds_start": 64,
"cds_end": null,
"cds_length": 846,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 5313,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile",
"transcript": "XM_017016912.3",
"protein_id": "XP_016872401.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 243,
"cds_start": 64,
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"cdna_start": 273,
"cdna_end": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "n.64T>A",
"hgvs_p": null,
"transcript": "ENST00000630487.2",
"protein_id": "ENSP00000486859.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1114,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "n.64T>A",
"hgvs_p": null,
"transcript": "ENST00000635953.1",
"protein_id": "ENSP00000490058.1",
"transcript_support_level": 5,
"aa_start": null,
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"cds_start": -4,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "n.64T>A",
"hgvs_p": null,
"transcript": "ENST00000636232.1",
"protein_id": "ENSP00000490325.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 2167,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "n.64T>A",
"hgvs_p": null,
"transcript": "ENST00000636754.1",
"protein_id": "ENSP00000489781.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 2200,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "n.64T>A",
"hgvs_p": null,
"transcript": "ENST00000636946.1",
"protein_id": "ENSP00000490654.1",
"transcript_support_level": 5,
"aa_start": null,
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"cds_start": -4,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "n.64T>A",
"hgvs_p": null,
"transcript": "ENST00000637037.1",
"protein_id": "ENSP00000490860.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "n.64T>A",
"hgvs_p": null,
"transcript": "ENST00000637611.1",
"protein_id": "ENSP00000489682.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "n.64T>A",
"hgvs_p": null,
"transcript": "ENST00000637925.1",
"protein_id": "ENSP00000489763.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI1",
"gene_hgnc_id": 6572,
"hgvs_c": "n.64T>A",
"hgvs_p": null,
"transcript": "ENST00000638049.1",
"protein_id": "ENSP00000490597.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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},
{
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],
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},
{
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],
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},
{
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"upstream_gene_variant"
],
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"gene_symbol": "ENSG00000303320",
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}
],
"gene_symbol": "LGI1",
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"dbsnp": "rs2133975421",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
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"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.20973917841911316,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.203,
"revel_prediction": "Benign",
"alphamissense_score": 0.0582,
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"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.121,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": 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_005097.4",
"gene_symbol": "LGI1",
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"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.64T>A",
"hgvs_p": "p.Phe22Ile"
},
{
"score": 0,
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"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000793618.1",
"gene_symbol": "ENSG00000303320",
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"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-110A>T",
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}
],
"clinvar_disease": "Autosomal dominant epilepsy with auditory features",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Autosomal dominant epilepsy with auditory features",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}