4-185514289-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014476.6(PDLIM3):c.379G>A(p.Val127Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00508 in 1,614,126 control chromosomes in the GnomAD database, including 338 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_014476.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0271 AC: 4116AN: 152120Hom.: 183 Cov.: 32
GnomAD3 exomes AF: 0.00725 AC: 1824AN: 251468Hom.: 75 AF XY: 0.00515 AC XY: 700AN XY: 135904
GnomAD4 exome AF: 0.00279 AC: 4079AN: 1461888Hom.: 153 Cov.: 33 AF XY: 0.00235 AC XY: 1711AN XY: 727248
GnomAD4 genome AF: 0.0271 AC: 4123AN: 152238Hom.: 185 Cov.: 32 AF XY: 0.0258 AC XY: 1921AN XY: 74450
ClinVar
Submissions by phenotype
not specified Benign:5
- -
- -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
- -
p.Val127Met in exon 4 of PDLIM3: This variant is not expected to have clinical s ignificance because it has been identified in 9.9% (437/4406) of African America n chromosomes from a broad population by the NHLBI Exome Sequencing Project (htt p://evs.gs.washington.edu/EVS; dbSNP rs11944325). -
not provided Benign:1Other:1
- -
- -
Primary dilated cardiomyopathy;C0007194:Hypertrophic cardiomyopathy Benign:1
- -
Cardiovascular phenotype Benign:1
General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at