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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: X-41531085-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=41531085&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 41531085,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000378163.7",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2442G>A",
"hgvs_p": "p.Ala814Ala",
"transcript": "NM_001367721.1",
"protein_id": "NP_001354650.1",
"transcript_support_level": null,
"aa_start": 814,
"aa_end": null,
"aa_length": 926,
"cds_start": 2442,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 3008,
"cdna_end": null,
"cdna_length": 8833,
"mane_select": "ENST00000378163.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2442G>A",
"hgvs_p": "p.Ala814Ala",
"transcript": "ENST00000378163.7",
"protein_id": "ENSP00000367405.1",
"transcript_support_level": 5,
"aa_start": 814,
"aa_end": null,
"aa_length": 926,
"cds_start": 2442,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 3008,
"cdna_end": null,
"cdna_length": 8833,
"mane_select": "NM_001367721.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2373G>A",
"hgvs_p": "p.Ala791Ala",
"transcript": "ENST00000421587.8",
"protein_id": "ENSP00000400526.4",
"transcript_support_level": 1,
"aa_start": 791,
"aa_end": null,
"aa_length": 903,
"cds_start": 2373,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 2395,
"cdna_end": null,
"cdna_length": 8220,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2340G>A",
"hgvs_p": "p.Ala780Ala",
"transcript": "ENST00000378166.9",
"protein_id": "ENSP00000367408.5",
"transcript_support_level": 1,
"aa_start": 780,
"aa_end": null,
"aa_length": 892,
"cds_start": 2340,
"cds_end": null,
"cds_length": 2679,
"cdna_start": 2382,
"cdna_end": null,
"cdna_length": 3244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2304G>A",
"hgvs_p": "p.Ala768Ala",
"transcript": "ENST00000442742.7",
"protein_id": "ENSP00000398007.3",
"transcript_support_level": 1,
"aa_start": 768,
"aa_end": null,
"aa_length": 880,
"cds_start": 2304,
"cds_end": null,
"cds_length": 2643,
"cdna_start": 2477,
"cdna_end": null,
"cdna_length": 3758,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "n.1708G>A",
"hgvs_p": null,
"transcript": "ENST00000378179.9",
"protein_id": null,
"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": 3240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2409G>A",
"hgvs_p": "p.Ala803Ala",
"transcript": "ENST00000645986.2",
"protein_id": "ENSP00000494409.2",
"transcript_support_level": null,
"aa_start": 803,
"aa_end": null,
"aa_length": 955,
"cds_start": 2409,
"cds_end": null,
"cds_length": 2868,
"cdna_start": 2938,
"cdna_end": null,
"cdna_length": 4550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2445G>A",
"hgvs_p": "p.Ala815Ala",
"transcript": "ENST00000378168.8",
"protein_id": "ENSP00000367410.4",
"transcript_support_level": 5,
"aa_start": 815,
"aa_end": null,
"aa_length": 927,
"cds_start": 2445,
"cds_end": null,
"cds_length": 2784,
"cdna_start": 2974,
"cdna_end": null,
"cdna_length": 8799,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2427G>A",
"hgvs_p": "p.Ala809Ala",
"transcript": "NM_003688.4",
"protein_id": "NP_003679.2",
"transcript_support_level": null,
"aa_start": 809,
"aa_end": null,
"aa_length": 921,
"cds_start": 2427,
"cds_end": null,
"cds_length": 2766,
"cdna_start": 2993,
"cdna_end": null,
"cdna_length": 8818,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2427G>A",
"hgvs_p": "p.Ala809Ala",
"transcript": "ENST00000645566.1",
"protein_id": "ENSP00000494788.1",
"transcript_support_level": null,
"aa_start": 809,
"aa_end": null,
"aa_length": 921,
"cds_start": 2427,
"cds_end": null,
"cds_length": 2766,
"cdna_start": 2454,
"cdna_end": null,
"cdna_length": 4002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2424G>A",
"hgvs_p": "p.Ala808Ala",
"transcript": "NM_001410745.1",
"protein_id": "NP_001397674.1",
"transcript_support_level": null,
"aa_start": 808,
"aa_end": null,
"aa_length": 920,
"cds_start": 2424,
"cds_end": null,
"cds_length": 2763,
"cdna_start": 2990,
"cdna_end": null,
"cdna_length": 8815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2424G>A",
"hgvs_p": "p.Ala808Ala",
"transcript": "ENST00000644219.1",
"protein_id": "ENSP00000495357.1",
"transcript_support_level": null,
"aa_start": 808,
"aa_end": null,
"aa_length": 920,
"cds_start": 2424,
"cds_end": null,
"cds_length": 2763,
"cdna_start": 2597,
"cdna_end": null,
"cdna_length": 6048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2391G>A",
"hgvs_p": "p.Ala797Ala",
"transcript": "ENST00000378154.3",
"protein_id": "ENSP00000367396.2",
"transcript_support_level": 5,
"aa_start": 797,
"aa_end": null,
"aa_length": 909,
"cds_start": 2391,
"cds_end": null,
"cds_length": 2730,
"cdna_start": 2832,
"cdna_end": null,
"cdna_length": 4037,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2388G>A",
"hgvs_p": "p.Ala796Ala",
"transcript": "ENST00000378158.6",
"protein_id": "ENSP00000367400.2",
"transcript_support_level": 5,
"aa_start": 796,
"aa_end": null,
"aa_length": 908,
"cds_start": 2388,
"cds_end": null,
"cds_length": 2727,
"cdna_start": 2544,
"cdna_end": null,
"cdna_length": 3754,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2376G>A",
"hgvs_p": "p.Ala792Ala",
"transcript": "ENST00000675354.1",
"protein_id": "ENSP00000502315.1",
"transcript_support_level": null,
"aa_start": 792,
"aa_end": null,
"aa_length": 904,
"cds_start": 2376,
"cds_end": null,
"cds_length": 2715,
"cdna_start": 2905,
"cdna_end": null,
"cdna_length": 8730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2358G>A",
"hgvs_p": "p.Ala786Ala",
"transcript": "NM_001126054.3",
"protein_id": "NP_001119526.1",
"transcript_support_level": null,
"aa_start": 786,
"aa_end": null,
"aa_length": 898,
"cds_start": 2358,
"cds_end": null,
"cds_length": 2697,
"cdna_start": 2924,
"cdna_end": null,
"cdna_length": 8749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2358G>A",
"hgvs_p": "p.Ala786Ala",
"transcript": "ENST00000646120.2",
"protein_id": "ENSP00000495291.2",
"transcript_support_level": null,
"aa_start": 786,
"aa_end": null,
"aa_length": 898,
"cds_start": 2358,
"cds_end": null,
"cds_length": 2697,
"cdna_start": 2377,
"cdna_end": null,
"cdna_length": 3239,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2355G>A",
"hgvs_p": "p.Ala785Ala",
"transcript": "NM_001126055.3",
"protein_id": "NP_001119527.1",
"transcript_support_level": null,
"aa_start": 785,
"aa_end": null,
"aa_length": 897,
"cds_start": 2355,
"cds_end": null,
"cds_length": 2694,
"cdna_start": 2921,
"cdna_end": null,
"cdna_length": 8746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2355G>A",
"hgvs_p": "p.Ala785Ala",
"transcript": "ENST00000644347.1",
"protein_id": "ENSP00000494183.1",
"transcript_support_level": null,
"aa_start": 785,
"aa_end": null,
"aa_length": 897,
"cds_start": 2355,
"cds_end": null,
"cds_length": 2694,
"cdna_start": 2536,
"cdna_end": null,
"cdna_length": 8361,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1764G>A",
"hgvs_p": "p.Ala588Ala",
"transcript": "ENST00000646087.2",
"protein_id": "ENSP00000495510.2",
"transcript_support_level": null,
"aa_start": 588,
"aa_end": null,
"aa_length": 700,
"cds_start": 1764,
"cds_end": null,
"cds_length": 2103,
"cdna_start": 1898,
"cdna_end": null,
"cdna_length": 3392,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.213G>A",
"hgvs_p": "p.Ala71Ala",
"transcript": "ENST00000643733.1",
"protein_id": "ENSP00000496319.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 192,
"cds_start": 213,
"cds_end": null,
"cds_length": 579,
"cdna_start": 214,
"cdna_end": null,
"cdna_length": 667,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2442G>A",
"hgvs_p": "p.Ala814Ala",
"transcript": "XM_011543993.3",
"protein_id": "XP_011542295.1",
"transcript_support_level": null,
"aa_start": 814,
"aa_end": null,
"aa_length": 926,
"cds_start": 2442,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 2488,
"cdna_end": null,
"cdna_length": 8313,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.2406G>A",
"hgvs_p": "p.Ala802Ala",
"transcript": "XM_011543994.3",
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},
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},
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"hgvs_p": "p.Ala773Ala",
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},
{
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"hgvs_c": "c.1869G>A",
"hgvs_p": "p.Ala623Ala",
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},
{
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"consequences": [
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],
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"gene_symbol": "CASK",
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"hgvs_c": "n.1221G>A",
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},
{
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],
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"gene_symbol": "CASK",
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"hgvs_c": "n.2673G>A",
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"transcript": "ENST00000645937.2",
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"cds_start": -4,
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"biotype": null,
"feature": null
}
],
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"dbsnp": "rs141158465",
"frequency_reference_population": 0.0010598869,
"hom_count_reference_population": 713,
"allele_count_reference_population": 1282,
"gnomad_exomes_af": 0.00111434,
"gnomad_genomes_af": 0.000526518,
"gnomad_exomes_ac": 1223,
"gnomad_genomes_ac": 59,
"gnomad_exomes_homalt": 13,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8199999928474426,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.82,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.919,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000378163.7",
"gene_symbol": "CASK",
"hgnc_id": 1497,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.2442G>A",
"hgvs_p": "p.Ala814Ala"
}
],
"clinvar_disease": " CASK-related, X-linked,CASK-related disorder,Inborn genetic diseases,Intellectual disability,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|Intellectual disability, CASK-related, X-linked|not provided|Inborn genetic diseases|CASK-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}