15-74956144-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017793.3(RPP25):c.440G>T(p.Arg147Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 1,450,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_017793.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPP25 | NM_017793.3 | c.440G>T | p.Arg147Leu | missense_variant | Exon 1 of 1 | ENST00000322177.6 | NP_060263.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152214Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.0000523 AC: 12AN: 229566Hom.: 0 AF XY: 0.0000399 AC XY: 5AN XY: 125238
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1450816Hom.: 0 Cov.: 30 AF XY: 0.00000971 AC XY: 7AN XY: 721028
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.440G>T (p.R147L) alteration is located in exon 1 (coding exon 1) of the RPP25 gene. This alteration results from a G to T substitution at nucleotide position 440, causing the arginine (R) at amino acid position 147 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at