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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-11765481-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=11765481&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 11765481,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000312196.10",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "NM_078629.4",
"protein_id": "NP_523353.2",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 521,
"cds_start": 923,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 950,
"cdna_end": null,
"cdna_length": 2286,
"mane_select": "ENST00000312196.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000312196.10",
"protein_id": "ENSP00000312244.4",
"transcript_support_level": 1,
"aa_start": 308,
"aa_end": null,
"aa_length": 521,
"cds_start": 923,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 950,
"cdna_end": null,
"cdna_length": 2286,
"mane_select": "NM_078629.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.920T>C",
"hgvs_p": "p.Leu307Pro",
"transcript": "ENST00000647869.1",
"protein_id": "ENSP00000497615.1",
"transcript_support_level": null,
"aa_start": 307,
"aa_end": null,
"aa_length": 520,
"cds_start": 920,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 979,
"cdna_end": null,
"cdna_length": 2171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.887T>C",
"hgvs_p": "p.Leu296Pro",
"transcript": "NM_001193270.2",
"protein_id": "NP_001180199.1",
"transcript_support_level": null,
"aa_start": 296,
"aa_end": null,
"aa_length": 509,
"cds_start": 887,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 1013,
"cdna_end": null,
"cdna_length": 2330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.887T>C",
"hgvs_p": "p.Leu296Pro",
"transcript": "ENST00000398527.7",
"protein_id": "ENSP00000381538.2",
"transcript_support_level": 2,
"aa_start": 296,
"aa_end": null,
"aa_length": 509,
"cds_start": 887,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 1039,
"cdna_end": null,
"cdna_length": 2329,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.821T>C",
"hgvs_p": "p.Leu274Pro",
"transcript": "ENST00000649130.1",
"protein_id": "ENSP00000497949.1",
"transcript_support_level": null,
"aa_start": 274,
"aa_end": null,
"aa_length": 487,
"cds_start": 821,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 823,
"cdna_end": null,
"cdna_length": 2027,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000647857.1",
"protein_id": "ENSP00000497753.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 431,
"cds_start": 923,
"cds_end": null,
"cds_length": 1296,
"cdna_start": 937,
"cdna_end": null,
"cdna_length": 1715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "NM_078628.2",
"protein_id": "NP_523352.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 416,
"cds_start": 923,
"cds_end": null,
"cds_length": 1251,
"cdna_start": 950,
"cdna_end": null,
"cdna_length": 3446,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000337339.7",
"protein_id": "ENSP00000338078.2",
"transcript_support_level": 2,
"aa_start": 308,
"aa_end": null,
"aa_length": 416,
"cds_start": 923,
"cds_end": null,
"cds_length": 1251,
"cdna_start": 984,
"cdna_end": null,
"cdna_length": 3480,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.476T>C",
"hgvs_p": "p.Leu159Pro",
"transcript": "NM_001282174.1",
"protein_id": "NP_001269103.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 372,
"cds_start": 476,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 945,
"cdna_end": null,
"cdna_length": 2262,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.476T>C",
"hgvs_p": "p.Leu159Pro",
"transcript": "ENST00000361672.6",
"protein_id": "ENSP00000354562.2",
"transcript_support_level": 2,
"aa_start": 159,
"aa_end": null,
"aa_length": 372,
"cds_start": 476,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 945,
"cdna_end": null,
"cdna_length": 2256,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.476T>C",
"hgvs_p": "p.Leu159Pro",
"transcript": "ENST00000649649.1",
"protein_id": "ENSP00000497137.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 372,
"cds_start": 476,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 801,
"cdna_end": null,
"cdna_length": 2085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.476T>C",
"hgvs_p": "p.Leu159Pro",
"transcript": "ENST00000649685.1",
"protein_id": "ENSP00000497496.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 372,
"cds_start": 476,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 817,
"cdna_end": null,
"cdna_length": 1788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.476T>C",
"hgvs_p": "p.Leu159Pro",
"transcript": "ENST00000650215.1",
"protein_id": "ENSP00000496944.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 372,
"cds_start": 476,
"cds_end": null,
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"cdna_start": 905,
"cdna_end": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.425T>C",
"hgvs_p": "p.Leu142Pro",
"transcript": "NM_006800.4",
"protein_id": "NP_006791.2",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 355,
"cds_start": 425,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 967,
"cdna_end": null,
"cdna_length": 2303,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.425T>C",
"hgvs_p": "p.Leu142Pro",
"transcript": "ENST00000482871.6",
"protein_id": "ENSP00000498064.1",
"transcript_support_level": 3,
"aa_start": 142,
"aa_end": null,
"aa_length": 355,
"cds_start": 425,
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"cdna_start": 1098,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.425T>C",
"hgvs_p": "p.Leu142Pro",
"transcript": "ENST00000648013.1",
"protein_id": "ENSP00000497518.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 355,
"cds_start": 425,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 934,
"cdna_end": null,
"cdna_length": 2163,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.425T>C",
"hgvs_p": "p.Leu142Pro",
"transcript": "ENST00000649078.1",
"protein_id": "ENSP00000498017.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 355,
"cds_start": 425,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 1190,
"cdna_end": null,
"cdna_length": 2507,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.425T>C",
"hgvs_p": "p.Leu142Pro",
"transcript": "ENST00000649271.1",
"protein_id": "ENSP00000496967.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
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},
{
"aa_ref": "L",
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.425T>C",
"hgvs_p": "p.Leu142Pro",
"transcript": "ENST00000649602.1",
"protein_id": "ENSP00000498168.1",
"transcript_support_level": null,
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"aa_end": null,
"aa_length": 355,
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"feature": null
},
{
"aa_ref": "L",
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.425T>C",
"hgvs_p": "p.Leu142Pro",
"transcript": "ENST00000650628.1",
"protein_id": "ENSP00000496838.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
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"cds_start": 425,
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"cdna_start": 790,
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"cdna_length": 2053,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.422T>C",
"hgvs_p": "p.Leu141Pro",
"transcript": "ENST00000380693.8",
"protein_id": "ENSP00000370069.4",
"transcript_support_level": 2,
"aa_start": 141,
"aa_end": null,
"aa_length": 354,
"cds_start": 422,
"cds_end": null,
"cds_length": 1065,
"cdna_start": 977,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"hgvs_c": "c.425T>C",
"hgvs_p": "p.Leu142Pro",
"transcript": "ENST00000649797.1",
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},
{
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},
{
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"protein_id": "ENSP00000496974.1",
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},
{
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"upstream_gene_variant"
],
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"gene_symbol": "MSL3",
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"hgvs_c": "n.-119T>C",
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"transcript": "ENST00000649420.1",
"protein_id": "ENSP00000498117.1",
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"cdna_length": 524,
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}
],
"gene_symbol": "MSL3",
"gene_hgnc_id": 7370,
"dbsnp": "rs1555906707",
"frequency_reference_population": null,
"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,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.25802966952323914,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.163,
"revel_prediction": "Benign",
"alphamissense_score": 0.0983,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.021,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP5_Moderate,BP4",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 1,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP5_Moderate",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000312196.10",
"gene_symbol": "MSL3",
"hgnc_id": 7370,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro"
}
],
"clinvar_disease": "Basilicata-Akhtar syndrome,Intellectual disability",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Basilicata-Akhtar syndrome|Intellectual disability",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}