4-185502282-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014476.6(PDLIM3):c.*12C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0116 in 1,613,670 control chromosomes in the GnomAD database, including 164 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_014476.6 3_prime_UTR
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: 0.00930 AC: 1414AN: 152006Hom.: 17 Cov.: 33
GnomAD3 exomes AF: 0.0111 AC: 2799AN: 251472Hom.: 30 AF XY: 0.0119 AC XY: 1621AN XY: 135912
GnomAD4 exome AF: 0.0119 AC: 17351AN: 1461546Hom.: 147 Cov.: 30 AF XY: 0.0122 AC XY: 8891AN XY: 727108
GnomAD4 genome AF: 0.00930 AC: 1414AN: 152124Hom.: 17 Cov.: 33 AF XY: 0.00896 AC XY: 666AN XY: 74368
ClinVar
Submissions by phenotype
not specified Benign:3
*12C>T in exon 8 of PDLIM3: This variant is not expected to have clinical signif icance because it has been identified in 1.3% (111/8600) of European American ch romosomes from a broad population by the NHLBI Exome Sequencing Project (http:// evs.gs.washington.edu/EVS; dbSNP rs8315). -
- -
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. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at