rs150317928
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001167.4(XIAP):āc.455C>Gā(p.Thr152Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,209,888 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 12 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_001167.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XIAP | NM_001167.4 | c.455C>G | p.Thr152Ser | missense_variant | 2/7 | ENST00000371199.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XIAP | ENST00000371199.8 | c.455C>G | p.Thr152Ser | missense_variant | 2/7 | 1 | NM_001167.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000179 AC: 20AN: 111774Hom.: 0 Cov.: 23 AF XY: 0.000118 AC XY: 4AN XY: 33954
GnomAD3 exomes AF: 0.0000546 AC: 10AN: 183083Hom.: 0 AF XY: 0.0000592 AC XY: 4AN XY: 67609
GnomAD4 exome AF: 0.0000200 AC: 22AN: 1098114Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 8AN XY: 363482
GnomAD4 genome ? AF: 0.000179 AC: 20AN: 111774Hom.: 0 Cov.: 23 AF XY: 0.000118 AC XY: 4AN XY: 33954
ClinVar
Submissions by phenotype
X-linked lymphoproliferative disease due to XIAP deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at