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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-53235017-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=53235017&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 53235017,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000642864.1",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3669G>A",
"hgvs_p": "p.Pro1223Pro",
"transcript": "NM_001111125.3",
"protein_id": "NP_001104595.1",
"transcript_support_level": null,
"aa_start": 1223,
"aa_end": null,
"aa_length": 1488,
"cds_start": 3669,
"cds_end": null,
"cds_length": 4467,
"cdna_start": 3896,
"cdna_end": null,
"cdna_length": 6037,
"mane_select": "ENST00000642864.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3669G>A",
"hgvs_p": "p.Pro1223Pro",
"transcript": "ENST00000642864.1",
"protein_id": "ENSP00000495726.1",
"transcript_support_level": null,
"aa_start": 1223,
"aa_end": null,
"aa_length": 1488,
"cds_start": 3669,
"cds_end": null,
"cds_length": 4467,
"cdna_start": 3896,
"cdna_end": null,
"cdna_length": 6037,
"mane_select": "NM_001111125.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.*154G>A",
"hgvs_p": null,
"transcript": "ENST00000375365.2",
"protein_id": "ENSP00000364514.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 949,
"cds_start": -4,
"cds_end": null,
"cds_length": 2850,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4004,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3828G>A",
"hgvs_p": "p.Pro1276Pro",
"transcript": "ENST00000706952.1",
"protein_id": "ENSP00000516672.1",
"transcript_support_level": null,
"aa_start": 1276,
"aa_end": null,
"aa_length": 1541,
"cds_start": 3828,
"cds_end": null,
"cds_length": 4626,
"cdna_start": 3828,
"cdna_end": null,
"cdna_length": 5969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3669G>A",
"hgvs_p": "p.Pro1223Pro",
"transcript": "ENST00000674510.1",
"protein_id": "ENSP00000502054.1",
"transcript_support_level": null,
"aa_start": 1223,
"aa_end": null,
"aa_length": 1488,
"cds_start": 3669,
"cds_end": null,
"cds_length": 4467,
"cdna_start": 3870,
"cdna_end": null,
"cdna_length": 6011,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3639G>A",
"hgvs_p": "p.Pro1213Pro",
"transcript": "ENST00000675719.1",
"protein_id": "ENSP00000501927.1",
"transcript_support_level": null,
"aa_start": 1213,
"aa_end": null,
"aa_length": 1478,
"cds_start": 3639,
"cds_end": null,
"cds_length": 4437,
"cdna_start": 3866,
"cdna_end": null,
"cdna_length": 6008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3765G>A",
"hgvs_p": "p.Pro1255Pro",
"transcript": "XM_006724579.4",
"protein_id": "XP_006724642.1",
"transcript_support_level": null,
"aa_start": 1255,
"aa_end": null,
"aa_length": 1520,
"cds_start": 3765,
"cds_end": null,
"cds_length": 4563,
"cdna_start": 3992,
"cdna_end": null,
"cdna_length": 6133,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3171G>A",
"hgvs_p": "p.Pro1057Pro",
"transcript": "XM_017029360.2",
"protein_id": "XP_016884849.1",
"transcript_support_level": null,
"aa_start": 1057,
"aa_end": null,
"aa_length": 1322,
"cds_start": 3171,
"cds_end": null,
"cds_length": 3969,
"cdna_start": 3234,
"cdna_end": null,
"cdna_length": 5375,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3054G>A",
"hgvs_p": "p.Pro1018Pro",
"transcript": "XM_006724580.4",
"protein_id": "XP_006724643.1",
"transcript_support_level": null,
"aa_start": 1018,
"aa_end": null,
"aa_length": 1283,
"cds_start": 3054,
"cds_end": null,
"cds_length": 3852,
"cdna_start": 3117,
"cdna_end": null,
"cdna_length": 5258,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2958G>A",
"hgvs_p": "p.Pro986Pro",
"transcript": "XM_011530773.3",
"protein_id": "XP_011529075.1",
"transcript_support_level": null,
"aa_start": 986,
"aa_end": null,
"aa_length": 1251,
"cds_start": 2958,
"cds_end": null,
"cds_length": 3756,
"cdna_start": 3021,
"cdna_end": null,
"cdna_length": 5162,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.*154G>A",
"hgvs_p": null,
"transcript": "NM_001410736.1",
"protein_id": "NP_001397665.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1154,
"cds_start": -4,
"cds_end": null,
"cds_length": 3465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.*154G>A",
"hgvs_p": null,
"transcript": "ENST00000640694.1",
"protein_id": "ENSP00000492403.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1154,
"cds_start": -4,
"cds_end": null,
"cds_length": 3465,
"cdna_start": null,
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"cdna_length": 5958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.*154G>A",
"hgvs_p": null,
"transcript": "NM_001441093.1",
"protein_id": "NP_001428022.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 988,
"cds_start": -4,
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"cds_length": 2967,
"cdna_start": null,
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"cdna_length": 5325,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.*154G>A",
"hgvs_p": null,
"transcript": "NM_015075.2",
"protein_id": "NP_055890.1",
"transcript_support_level": null,
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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": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.*154G>A",
"hgvs_p": null,
"transcript": "NM_001441094.1",
"protein_id": "NP_001428023.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 917,
"cds_start": -4,
"cds_end": null,
"cds_length": 2754,
"cdna_start": null,
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"cdna_length": 5112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.*154G>A",
"hgvs_p": null,
"transcript": "XM_006724584.4",
"protein_id": "XP_006724647.1",
"transcript_support_level": null,
"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": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3451+1305G>A",
"hgvs_p": null,
"transcript": "NM_001441092.1",
"protein_id": "NP_001428021.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1168,
"cds_start": -4,
"cds_end": null,
"cds_length": 3507,
"cdna_start": null,
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"cdna_length": 7654,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2740+1305G>A",
"hgvs_p": null,
"transcript": "NM_001441095.1",
"protein_id": "NP_001428024.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 931,
"cds_start": -4,
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"cds_length": 2796,
"cdna_start": null,
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"cdna_length": 6779,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1452+766G>A",
"hgvs_p": null,
"transcript": "ENST00000638521.1",
"protein_id": "ENSP00000492636.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.960+766G>A",
"hgvs_p": null,
"transcript": "ENST00000638869.1",
"protein_id": "ENSP00000491736.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 333,
"cds_start": -4,
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"cdna_start": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.514+1305G>A",
"hgvs_p": null,
"transcript": "ENST00000640005.1",
"protein_id": "ENSP00000491293.1",
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"aa_start": null,
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"aa_length": 189,
"cds_start": -4,
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"cds_length": 570,
"cdna_start": null,
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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": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.316+1305G>A",
"hgvs_p": null,
"transcript": "ENST00000639796.1",
"protein_id": "ENSP00000492252.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 111,
"cds_start": -4,
"cds_end": null,
"cds_length": 336,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2351,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3597+766G>A",
"hgvs_p": null,
"transcript": "XM_006724581.5",
"protein_id": "XP_006724644.1",
"transcript_support_level": null,
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},
{
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{
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],
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"exon_count": 15,
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"protein_id": "XP_006724646.1",
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"cdna_length": 7750,
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},
{
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],
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"gene_symbol": "IQSEC2",
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},
{
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"strand": true,
"consequences": [
"downstream_gene_variant"
],
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"exon_count": 5,
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"gene_symbol": "IQSEC2",
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},
{
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],
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"gene_symbol": "IQSEC2",
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"hgvs_c": "c.*470G>A",
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"transcript": "XM_011530774.4",
"protein_id": "XP_011529076.1",
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"cdna_length": 4167,
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"feature": null
}
],
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"dbsnp": "rs782744933",
"frequency_reference_population": 0.000059804206,
"hom_count_reference_population": 22,
"allele_count_reference_population": 69,
"gnomad_exomes_af": 0.0000324579,
"gnomad_genomes_af": 0.000329396,
"gnomad_exomes_ac": 34,
"gnomad_genomes_ac": 35,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4699999988079071,
"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": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.55,
"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": "ENST00000642864.1",
"gene_symbol": "IQSEC2",
"hgnc_id": 29059,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.3669G>A",
"hgvs_p": "p.Pro1223Pro"
}
],
"clinvar_disease": " X-linked 1,IQSEC2-related disorder,Inborn genetic diseases,Intellectual disability,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4",
"phenotype_combined": "Intellectual disability, X-linked 1|not provided|IQSEC2-related disorder|Inborn genetic diseases",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}