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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-41636647-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=41636647&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 41636647,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000378163.7",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "NM_001367721.1",
"protein_id": "NP_001354650.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 926,
"cds_start": 846,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 1412,
"cdna_end": null,
"cdna_length": 8833,
"mane_select": "ENST00000378163.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "ENST00000378163.7",
"protein_id": "ENSP00000367405.1",
"transcript_support_level": 5,
"aa_start": 282,
"aa_end": null,
"aa_length": 926,
"cds_start": 846,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 1412,
"cdna_end": null,
"cdna_length": 8833,
"mane_select": "NM_001367721.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.864C>T",
"hgvs_p": "p.Tyr288Tyr",
"transcript": "ENST00000421587.8",
"protein_id": "ENSP00000400526.4",
"transcript_support_level": 1,
"aa_start": 288,
"aa_end": null,
"aa_length": 903,
"cds_start": 864,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 886,
"cdna_end": null,
"cdna_length": 8220,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "ENST00000378166.9",
"protein_id": "ENSP00000367408.5",
"transcript_support_level": 1,
"aa_start": 282,
"aa_end": null,
"aa_length": 892,
"cds_start": 846,
"cds_end": null,
"cds_length": 2679,
"cdna_start": 888,
"cdna_end": null,
"cdna_length": 3244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "ENST00000442742.7",
"protein_id": "ENSP00000398007.3",
"transcript_support_level": 1,
"aa_start": 282,
"aa_end": null,
"aa_length": 880,
"cds_start": 846,
"cds_end": null,
"cds_length": 2643,
"cdna_start": 1019,
"cdna_end": null,
"cdna_length": 3758,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "ENST00000645986.2",
"protein_id": "ENSP00000494409.2",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 955,
"cds_start": 846,
"cds_end": null,
"cds_length": 2868,
"cdna_start": 1375,
"cdna_end": null,
"cdna_length": 4550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.864C>T",
"hgvs_p": "p.Tyr288Tyr",
"transcript": "ENST00000378168.8",
"protein_id": "ENSP00000367410.4",
"transcript_support_level": 5,
"aa_start": 288,
"aa_end": null,
"aa_length": 927,
"cds_start": 864,
"cds_end": null,
"cds_length": 2784,
"cdna_start": 1393,
"cdna_end": null,
"cdna_length": 8799,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "NM_003688.4",
"protein_id": "NP_003679.2",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 921,
"cds_start": 846,
"cds_end": null,
"cds_length": 2766,
"cdna_start": 1412,
"cdna_end": null,
"cdna_length": 8818,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "ENST00000645566.1",
"protein_id": "ENSP00000494788.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 921,
"cds_start": 846,
"cds_end": null,
"cds_length": 2766,
"cdna_start": 873,
"cdna_end": null,
"cdna_length": 4002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "NM_001410745.1",
"protein_id": "NP_001397674.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 920,
"cds_start": 846,
"cds_end": null,
"cds_length": 2763,
"cdna_start": 1412,
"cdna_end": null,
"cdna_length": 8815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "ENST00000644219.1",
"protein_id": "ENSP00000495357.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 920,
"cds_start": 846,
"cds_end": null,
"cds_length": 2763,
"cdna_start": 1019,
"cdna_end": null,
"cdna_length": 6048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "ENST00000378154.3",
"protein_id": "ENSP00000367396.2",
"transcript_support_level": 5,
"aa_start": 282,
"aa_end": null,
"aa_length": 909,
"cds_start": 846,
"cds_end": null,
"cds_length": 2730,
"cdna_start": 1287,
"cdna_end": null,
"cdna_length": 4037,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "ENST00000378158.6",
"protein_id": "ENSP00000367400.2",
"transcript_support_level": 5,
"aa_start": 282,
"aa_end": null,
"aa_length": 908,
"cds_start": 846,
"cds_end": null,
"cds_length": 2727,
"cdna_start": 1002,
"cdna_end": null,
"cdna_length": 3754,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.864C>T",
"hgvs_p": "p.Tyr288Tyr",
"transcript": "ENST00000675354.1",
"protein_id": "ENSP00000502315.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 904,
"cds_start": 864,
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"cdna_start": 1393,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "NM_001126054.3",
"protein_id": "NP_001119526.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 898,
"cds_start": 846,
"cds_end": null,
"cds_length": 2697,
"cdna_start": 1412,
"cdna_end": null,
"cdna_length": 8749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "ENST00000646120.2",
"protein_id": "ENSP00000495291.2",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
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"cds_start": 846,
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"cdna_start": 865,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "NM_001126055.3",
"protein_id": "NP_001119527.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 897,
"cds_start": 846,
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"cds_length": 2694,
"cdna_start": 1412,
"cdna_end": null,
"cdna_length": 8746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "ENST00000644347.1",
"protein_id": "ENSP00000494183.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 897,
"cds_start": 846,
"cds_end": null,
"cds_length": 2694,
"cdna_start": 1027,
"cdna_end": null,
"cdna_length": 8361,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.291C>T",
"hgvs_p": "p.Tyr97Tyr",
"transcript": "ENST00000646087.2",
"protein_id": "ENSP00000495510.2",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 700,
"cds_start": 291,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.291C>T",
"hgvs_p": "p.Tyr97Tyr",
"transcript": "ENST00000643043.2",
"protein_id": "ENSP00000493518.2",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 393,
"cds_start": 291,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr",
"transcript": "ENST00000643831.2",
"protein_id": "ENSP00000494388.2",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 365,
"cds_start": 846,
"cds_end": null,
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"cdna_start": 1287,
"cdna_end": null,
"cdna_length": 1540,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.864C>T",
"hgvs_p": "p.Tyr288Tyr",
"transcript": "XM_011543993.3",
"protein_id": "XP_011542295.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 926,
"cds_start": 864,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 910,
"cdna_end": null,
"cdna_length": 8313,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.864C>T",
"hgvs_p": "p.Tyr288Tyr",
"transcript": "XM_011543994.3",
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},
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},
{
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}
],
"gene_symbol": "CASK",
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"dbsnp": "rs886128077",
"frequency_reference_population": 0.000011038296,
"hom_count_reference_population": 1,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000938107,
"gnomad_genomes_af": 0.0000268476,
"gnomad_exomes_ac": 10,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.49000000953674316,
"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": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.89,
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000378163.7",
"gene_symbol": "CASK",
"hgnc_id": 1497,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.846C>T",
"hgvs_p": "p.Tyr282Tyr"
},
{
"score": -10,
"benign_score": 12,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "XR_007068219.1",
"gene_symbol": "LOC124905180",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.335-10885G>A",
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}
],
"clinvar_disease": " CASK-related, X-linked,Intellectual disability,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "not provided|Intellectual disability, CASK-related, X-linked",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}