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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: 1-41009413-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=41009413&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 41009413,
"ref": "A",
"alt": "G",
"effect": "intron_variant",
"transcript": "ENST00000650070.2",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.1547-32A>G",
"hgvs_p": null,
"transcript": "NM_001905.4",
"protein_id": "NP_001896.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 591,
"cds_start": -4,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2840,
"mane_select": "ENST00000650070.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.1547-32A>G",
"hgvs_p": null,
"transcript": "ENST00000650070.2",
"protein_id": "ENSP00000497602.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 591,
"cds_start": -4,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2840,
"mane_select": "NM_001905.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.1547-32A>G",
"hgvs_p": null,
"transcript": "ENST00000372616.1",
"protein_id": "ENSP00000361699.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 591,
"cds_start": -4,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2037,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.1547-32A>G",
"hgvs_p": null,
"transcript": "ENST00000470271.6",
"protein_id": "ENSP00000497901.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 591,
"cds_start": -4,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3212,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.1547-32A>G",
"hgvs_p": null,
"transcript": "ENST00000649124.2",
"protein_id": "ENSP00000497744.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 591,
"cds_start": -4,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2972,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.1547-32A>G",
"hgvs_p": null,
"transcript": "ENST00000649864.1",
"protein_id": "ENSP00000496792.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 564,
"cds_start": -4,
"cds_end": null,
"cds_length": 1695,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.1079-32A>G",
"hgvs_p": null,
"transcript": "NM_001301237.2",
"protein_id": "NP_001288166.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 435,
"cds_start": -4,
"cds_end": null,
"cds_length": 1308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.1079-32A>G",
"hgvs_p": null,
"transcript": "ENST00000649215.1",
"protein_id": "ENSP00000497698.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 435,
"cds_start": -4,
"cds_end": null,
"cds_length": 1308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1821,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.854-32A>G",
"hgvs_p": null,
"transcript": "ENST00000696070.1",
"protein_id": "ENSP00000512372.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 360,
"cds_start": -4,
"cds_end": null,
"cds_length": 1083,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1712,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "n.*553-32A>G",
"hgvs_p": null,
"transcript": "ENST00000463423.6",
"protein_id": "ENSP00000497446.1",
"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": 1389,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "n.499-32A>G",
"hgvs_p": null,
"transcript": "ENST00000464283.5",
"protein_id": null,
"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": 643,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "n.1684-32A>G",
"hgvs_p": null,
"transcript": "ENST00000480420.6",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
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"aa_length": null,
"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": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "n.4198-32A>G",
"hgvs_p": null,
"transcript": "ENST00000486889.2",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"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": [
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],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "n.1728-32A>G",
"hgvs_p": null,
"transcript": "ENST00000498694.2",
"protein_id": null,
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"aa_start": null,
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"feature": null
},
{
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"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "n.*1738-32A>G",
"hgvs_p": null,
"transcript": "ENST00000648020.2",
"protein_id": "ENSP00000497714.1",
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"aa_start": null,
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"aa_length": null,
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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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "n.2958-32A>G",
"hgvs_p": null,
"transcript": "ENST00000648801.1",
"protein_id": null,
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},
{
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],
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"gene_symbol": "CTPS1",
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"hgvs_c": "n.*94-32A>G",
"hgvs_p": null,
"transcript": "ENST00000648914.1",
"protein_id": "ENSP00000496963.1",
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"mane_select": null,
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"feature": null
},
{
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"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 19,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "n.3141-32A>G",
"hgvs_p": null,
"transcript": "ENST00000650634.2",
"protein_id": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "n.*94-32A>G",
"hgvs_p": null,
"transcript": "ENST00000696107.1",
"protein_id": "ENSP00000512401.1",
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"hgvs_c": "n.*281-32A>G",
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},
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"strand": true,
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],
"exon_rank": null,
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"intron_rank_end": null,
"gene_symbol": "CTPS1",
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"hgvs_c": "n.1891-32A>G",
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"transcript": "ENST00000696109.1",
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},
{
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"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "n.1773-32A>G",
"hgvs_p": null,
"transcript": "NR_125440.2",
"protein_id": null,
"transcript_support_level": null,
"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": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.1568-32A>G",
"hgvs_p": null,
"transcript": "XM_024453552.2",
"protein_id": "XP_024309320.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 598,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 18,
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"gene_symbol": "CTPS1",
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"hgvs_c": "c.1568-32A>G",
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"transcript": "XM_047447461.1",
"protein_id": "XP_047303417.1",
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"aa_end": null,
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"cds_start": -4,
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"cdna_length": 1934,
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"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
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"exon_count": 19,
"intron_rank": 16,
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"gene_symbol": "CTPS1",
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"hgvs_c": "c.1547-32A>G",
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"transcript": "XM_024453553.2",
"protein_id": "XP_024309321.1",
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"aa_start": null,
"aa_end": null,
"aa_length": 591,
"cds_start": -4,
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"cdna_length": 3238,
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"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
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"exon_count": 19,
"intron_rank": 16,
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"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.1547-32A>G",
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"transcript": "XM_024453554.1",
"protein_id": "XP_024309322.1",
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"aa_start": null,
"aa_end": null,
"aa_length": 591,
"cds_start": -4,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2778,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"dbsnp": "rs12144160",
"frequency_reference_population": 0.54630744,
"hom_count_reference_population": 232519,
"allele_count_reference_population": 834725,
"gnomad_exomes_af": 0.554201,
"gnomad_genomes_af": 0.474924,
"gnomad_exomes_ac": 762470,
"gnomad_genomes_ac": 72255,
"gnomad_exomes_homalt": 213902,
"gnomad_genomes_homalt": 18617,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8899999856948853,
"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": -0.89,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.823,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000650070.2",
"gene_symbol": "CTPS1",
"hgnc_id": 2519,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1547-32A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Severe combined immunodeficiency due to CTPS1 deficiency,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "Severe combined immunodeficiency due to CTPS1 deficiency|not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}