X-123885734-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001167.4(XIAP):āc.72A>Gā(p.Val24=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000089 in 112,354 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. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001167.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XIAP | NM_001167.4 | c.72A>G | p.Val24= | synonymous_variant | 2/7 | ENST00000371199.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XIAP | ENST00000371199.8 | c.72A>G | p.Val24= | synonymous_variant | 2/7 | 1 | NM_001167.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000890 AC: 1AN: 112354Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34508
GnomAD4 exome Cov.: 30
GnomAD4 genome AF: 0.00000890 AC: 1AN: 112354Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34508
ClinVar
Submissions by phenotype
X-linked lymphoproliferative disease due to XIAP deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 14, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at