1-145673685-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001201325.2(PDZK1):c.1187G>A(p.Arg396Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 7/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R396W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001201325.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 16AN: 148552Hom.: 0 Cov.: 24 FAILED QC
GnomAD3 exomes AF: 0.0000747 AC: 6AN: 80348Hom.: 0 AF XY: 0.0000513 AC XY: 2AN XY: 38994
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000241 AC: 35AN: 1454596Hom.: 0 Cov.: 30 AF XY: 0.0000249 AC XY: 18AN XY: 723766
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000108 AC: 16AN: 148666Hom.: 0 Cov.: 24 AF XY: 0.0000831 AC XY: 6AN XY: 72244
ClinVar
Submissions by phenotype
not specified 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