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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-53254526-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=53254526&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 53254526,
"ref": "T",
"alt": "C",
"effect": "splice_region_variant,intron_variant",
"transcript": "NM_001111125.3",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1401+4A>G",
"hgvs_p": null,
"transcript": "NM_001111125.3",
"protein_id": "NP_001104595.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1488,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1401+4A>G",
"hgvs_p": null,
"transcript": "ENST00000642864.1",
"protein_id": "ENSP00000495726.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1488,
"cds_start": null,
"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": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.786+4A>G",
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.690+4A>G",
"hgvs_p": null,
"transcript": "ENST00000638630.1",
"protein_id": "ENSP00000492390.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 255,
"cds_start": null,
"cds_end": null,
"cds_length": 770,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000638630.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1560+4A>G",
"hgvs_p": null,
"transcript": "ENST00000706952.1",
"protein_id": "ENSP00000516672.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1541,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1401+4A>G",
"hgvs_p": null,
"transcript": "ENST00000674510.1",
"protein_id": "ENSP00000502054.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1488,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1371+4A>G",
"hgvs_p": null,
"transcript": "ENST00000675719.1",
"protein_id": "ENSP00000501927.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1478,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1401+4A>G",
"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": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1401+4A>G",
"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": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1401+4A>G",
"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": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.903+4A>G",
"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": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.786+4A>G",
"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": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.690+4A>G",
"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": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.690+4A>G",
"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": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1497+4A>G",
"hgvs_p": null,
"transcript": "XM_006724579.4",
"protein_id": "XP_006724642.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1520,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.903+4A>G",
"hgvs_p": null,
"transcript": "XM_017029360.2",
"protein_id": "XP_016884849.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1322,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.786+4A>G",
"hgvs_p": null,
"transcript": "XM_006724580.4",
"protein_id": "XP_006724643.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1283,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.690+4A>G",
"hgvs_p": null,
"transcript": "XM_011530773.3",
"protein_id": "XP_011529075.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1251,
"cds_start": null,
"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,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1497+4A>G",
"hgvs_p": null,
"transcript": "XM_006724581.5",
"protein_id": "XP_006724644.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1244,
"cds_start": null,
"cds_end": null,
"cds_length": 3735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006724581.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1497+4A>G",
"hgvs_p": null,
"transcript": "XM_011530774.4",
"protein_id": "XP_011529076.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1222,
"cds_start": null,
"cds_end": null,
"cds_length": 3669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011530774.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1497+4A>G",
"hgvs_p": null,
"transcript": "XM_006724582.5",
"protein_id": "XP_006724645.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1212,
"cds_start": null,
"cds_end": null,
"cds_length": 3639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006724582.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "IQSEC2",
"gene_hgnc_id": 29059,
"hgvs_c": "c.1497+4A>G",
"hgvs_p": null,
"transcript": "XM_006724583.5",
"protein_id": "XP_006724646.1",
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{
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{
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"feature": "XM_006724584.4"
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{
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"feature": "XM_011530776.3"
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{
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{
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"biotype": "pseudogene",
"feature": "XR_938365.3"
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],
"gene_symbol": "IQSEC2",
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"dbsnp": "rs1556864509",
"frequency_reference_population": 0.0000018464442,
"hom_count_reference_population": 1,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000184644,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
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"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4000000059604645,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9079999923706055,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.804,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.998419720370368,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001111125.3",
"gene_symbol": "IQSEC2",
"hgnc_id": 29059,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1401+4A>G",
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}
],
"clinvar_disease": " X-linked 1,Intellectual disability,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not provided|Intellectual disability, X-linked 1",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}