X-123910026-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001167.4(XIAP):c.*2845C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 326,921 control chromosomes in the GnomAD database, including 5,175 homozygotes. There are 28,723 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.20 ( 1513 hom., 6692 hem., cov: 23)
Exomes 𝑓: 0.24 ( 3662 hom. 22031 hem. )
Consequence
XIAP
NM_001167.4 3_prime_UTR
NM_001167.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.234
Genes affected
XIAP (HGNC:592): (X-linked inhibitor of apoptosis) This gene encodes a protein that belongs to a family of apoptotic suppressor proteins. Members of this family share a conserved motif termed, baculovirus IAP repeat, which is necessary for their anti-apoptotic function. This protein functions through binding to tumor necrosis factor receptor-associated factors TRAF1 and TRAF2 and inhibits apoptosis induced by menadione, a potent inducer of free radicals, and interleukin 1-beta converting enzyme. This protein also inhibits at least two members of the caspase family of cell-death proteases, caspase-3 and caspase-7. Mutations in this gene are the cause of X-linked lymphoproliferative syndrome. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 2 and 11.[provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant X-123910026-C-T is Benign according to our data. Variant chrX-123910026-C-T is described in ClinVar as [Benign]. Clinvar id is 367816.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XIAP | NM_001167.4 | c.*2845C>T | 3_prime_UTR_variant | 7/7 | ENST00000371199.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XIAP | ENST00000371199.8 | c.*2845C>T | 3_prime_UTR_variant | 7/7 | 1 | NM_001167.4 | P1 | ||
XIAP | ENST00000355640.3 | c.*2845C>T | 3_prime_UTR_variant | 7/7 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.196 AC: 21758AN: 111056Hom.: 1513 Cov.: 23 AF XY: 0.201 AC XY: 6681AN XY: 33272
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GnomAD3 exomes AF: 0.242 AC: 23854AN: 98475Hom.: 1927 AF XY: 0.253 AC XY: 9186AN XY: 36281
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GnomAD4 exome AF: 0.237 AC: 51080AN: 215811Hom.: 3662 Cov.: 0 AF XY: 0.257 AC XY: 22031AN XY: 85871
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GnomAD4 genome ? AF: 0.196 AC: 21764AN: 111110Hom.: 1513 Cov.: 23 AF XY: 0.201 AC XY: 6692AN XY: 33336
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
X-linked lymphoproliferative disease due to XIAP deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at