12-19130072-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_001256470.2(PLEKHA5):c.111C>T(p.Thr37Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000716 in 1,591,418 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001256470.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152062Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000114 AC: 24AN: 210322Hom.: 1 AF XY: 0.000139 AC XY: 16AN XY: 114712
GnomAD4 exome AF: 0.0000743 AC: 107AN: 1439248Hom.: 1 Cov.: 31 AF XY: 0.0000994 AC XY: 71AN XY: 714470
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152170Hom.: 0 Cov.: 30 AF XY: 0.0000807 AC XY: 6AN XY: 74374
ClinVar
Submissions by phenotype
PLEKHA5-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at