chr11-799386-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_145886.4(PIDD1):c.2654G>A(p.Arg885Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000405 in 1,611,900 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_145886.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000236 AC: 36AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000849 AC: 210AN: 247414Hom.: 2 AF XY: 0.00110 AC XY: 148AN XY: 134480
GnomAD4 exome AF: 0.000423 AC: 617AN: 1459550Hom.: 8 Cov.: 31 AF XY: 0.000606 AC XY: 440AN XY: 726188
GnomAD4 genome AF: 0.000236 AC: 36AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.000389 AC XY: 29AN XY: 74492
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at