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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-53234263-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=53234263&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 53234263,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001111125.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.4423G>A",
"hgvs_p": "p.Ala1475Thr",
"transcript": "NM_001111125.3",
"protein_id": "NP_001104595.1",
"transcript_support_level": null,
"aa_start": 1475,
"aa_end": null,
"aa_length": 1488,
"cds_start": 4423,
"cds_end": null,
"cds_length": 4467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000642864.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001111125.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.4423G>A",
"hgvs_p": "p.Ala1475Thr",
"transcript": "ENST00000642864.1",
"protein_id": "ENSP00000495726.1",
"transcript_support_level": null,
"aa_start": 1475,
"aa_end": null,
"aa_length": 1488,
"cds_start": 4423,
"cds_end": null,
"cds_length": 4467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001111125.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000642864.1"
},
{
"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.*908G>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": null,
"cds_end": null,
"cds_length": 2850,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375365.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.4582G>A",
"hgvs_p": "p.Ala1528Thr",
"transcript": "ENST00000706952.1",
"protein_id": "ENSP00000516672.1",
"transcript_support_level": null,
"aa_start": 1528,
"aa_end": null,
"aa_length": 1541,
"cds_start": 4582,
"cds_end": null,
"cds_length": 4626,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000706952.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.4423G>A",
"hgvs_p": "p.Ala1475Thr",
"transcript": "ENST00000674510.1",
"protein_id": "ENSP00000502054.1",
"transcript_support_level": null,
"aa_start": 1475,
"aa_end": null,
"aa_length": 1488,
"cds_start": 4423,
"cds_end": null,
"cds_length": 4467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674510.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.4393G>A",
"hgvs_p": "p.Ala1465Thr",
"transcript": "ENST00000675719.1",
"protein_id": "ENSP00000501927.1",
"transcript_support_level": null,
"aa_start": 1465,
"aa_end": null,
"aa_length": 1478,
"cds_start": 4393,
"cds_end": null,
"cds_length": 4437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675719.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.4519G>A",
"hgvs_p": "p.Ala1507Thr",
"transcript": "XM_006724579.4",
"protein_id": "XP_006724642.1",
"transcript_support_level": null,
"aa_start": 1507,
"aa_end": null,
"aa_length": 1520,
"cds_start": 4519,
"cds_end": null,
"cds_length": 4563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006724579.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.3925G>A",
"hgvs_p": "p.Ala1309Thr",
"transcript": "XM_017029360.2",
"protein_id": "XP_016884849.1",
"transcript_support_level": null,
"aa_start": 1309,
"aa_end": null,
"aa_length": 1322,
"cds_start": 3925,
"cds_end": null,
"cds_length": 3969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029360.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.3808G>A",
"hgvs_p": "p.Ala1270Thr",
"transcript": "XM_006724580.4",
"protein_id": "XP_006724643.1",
"transcript_support_level": null,
"aa_start": 1270,
"aa_end": null,
"aa_length": 1283,
"cds_start": 3808,
"cds_end": null,
"cds_length": 3852,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006724580.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.3712G>A",
"hgvs_p": "p.Ala1238Thr",
"transcript": "XM_011530773.3",
"protein_id": "XP_011529075.1",
"transcript_support_level": null,
"aa_start": 1238,
"aa_end": null,
"aa_length": 1251,
"cds_start": 3712,
"cds_end": null,
"cds_length": 3756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011530773.3"
},
{
"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.*908G>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": null,
"cds_end": null,
"cds_length": 3465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001410736.1"
},
{
"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.*908G>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": null,
"cds_end": null,
"cds_length": 3465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000640694.1"
},
{
"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.*908G>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": null,
"cds_end": null,
"cds_length": 2967,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001441093.1"
},
{
"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.*908G>A",
"hgvs_p": null,
"transcript": "NM_015075.2",
"protein_id": "NP_055890.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 949,
"cds_start": null,
"cds_end": null,
"cds_length": 2850,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015075.2"
},
{
"aa_ref": null,
"aa_alt": null,
"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.*908G>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": null,
"cds_end": null,
"cds_length": 2754,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001441094.1"
},
{
"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.*908G>A",
"hgvs_p": null,
"transcript": "XM_006724584.4",
"protein_id": "XP_006724647.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1186,
"cds_start": null,
"cds_end": null,
"cds_length": 3561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006724584.4"
},
{
"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": 14,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.3451+2059G>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": null,
"cds_end": null,
"cds_length": 3507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001441092.1"
},
{
"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": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.2740+2059G>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": null,
"cds_end": null,
"cds_length": 2796,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001441095.1"
},
{
"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": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1452+1520G>A",
"hgvs_p": null,
"transcript": "ENST00000638521.1",
"protein_id": "ENSP00000492636.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 529,
"cds_start": null,
"cds_end": null,
"cds_length": 1590,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000638521.1"
},
{
"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": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.960+1520G>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": null,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000638869.1"
},
{
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.514+2059G>A",
"hgvs_p": null,
"transcript": "ENST00000640005.1",
"protein_id": "ENSP00000491293.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 189,
"cds_start": null,
"cds_end": null,
"cds_length": 570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000640005.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.316+2059G>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": null,
"cds_end": null,
"cds_length": 336,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000639796.1"
},
{
"aa_ref": null,
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{
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{
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{
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],
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"biotype": "protein_coding",
"feature": "XM_047441928.1"
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],
"gene_symbol": "IQSEC2",
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"dbsnp": "rs1242748501",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 0.00000102706,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.17266929149627686,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.049,
"revel_prediction": "Benign",
"alphamissense_score": 0.0738,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.74,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.796,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001111125.3",
"gene_symbol": "IQSEC2",
"hgnc_id": 29059,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
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"hgvs_p": "p.Ala1475Thr"
}
],
"clinvar_disease": "IQSEC2-related disorder",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "IQSEC2-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}