NM_006247.4:c.492G>A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_006247.4(PPP5C):c.492G>A(p.Ser164Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 1,601,346 control chromosomes in the GnomAD database, including 55,404 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_006247.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP5C | NM_006247.4 | c.492G>A | p.Ser164Ser | synonymous_variant | Exon 3 of 13 | ENST00000012443.9 | NP_006238.1 | |
PPP5C | NM_001204284.2 | c.492G>A | p.Ser164Ser | synonymous_variant | Exon 3 of 12 | NP_001191213.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.221 AC: 33668AN: 152102Hom.: 4309 Cov.: 33
GnomAD3 exomes AF: 0.218 AC: 48879AN: 223938Hom.: 5409 AF XY: 0.221 AC XY: 26739AN XY: 120856
GnomAD4 exome AF: 0.270 AC: 391502AN: 1449126Hom.: 51098 Cov.: 34 AF XY: 0.267 AC XY: 192353AN XY: 719848
GnomAD4 genome AF: 0.221 AC: 33672AN: 152220Hom.: 4306 Cov.: 33 AF XY: 0.216 AC XY: 16097AN XY: 74420
ClinVar
Submissions by phenotype
PPP5C-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