rs17334739
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001167.4(XIAP):c.1301-175T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 111,416 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., 0 hem., cov: 23)
Consequence
XIAP
NM_001167.4 intron
NM_001167.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.291
Publications
1 publications found
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]
XIAP Gene-Disease associations (from GenCC):
- X-linked lymphoproliferative disease due to XIAP deficiencyInheritance: XL Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.0000180 AC: 2AN: 111416Hom.: 0 Cov.: 23 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
111416
Hom.:
Cov.:
23
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.0000180 AC: 2AN: 111416Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33628 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
111416
Hom.:
Cov.:
23
AF XY:
AC XY:
0
AN XY:
33628
show subpopulations
African (AFR)
AF:
AC:
2
AN:
30664
American (AMR)
AF:
AC:
0
AN:
10399
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2645
East Asian (EAS)
AF:
AC:
0
AN:
3543
South Asian (SAS)
AF:
AC:
0
AN:
2681
European-Finnish (FIN)
AF:
AC:
0
AN:
5968
Middle Eastern (MID)
AF:
AC:
0
AN:
239
European-Non Finnish (NFE)
AF:
AC:
0
AN:
53107
Other (OTH)
AF:
AC:
0
AN:
1493
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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