11-36462352-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001160169.1(PRR5L):c.596C>T(p.Thr199Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001160169.1 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 |
---|---|---|---|---|---|---|---|---|
PRR5L | NM_001160167.2 | c.723C>T | p.His241His | synonymous_variant | Exon 9 of 9 | ENST00000530639.6 | NP_001153639.1 | |
PRR5L | NM_001160169.1 | c.596C>T | p.Thr199Ile | missense_variant | Exon 7 of 7 | NP_001153641.1 | ||
PRR5L | NM_024841.5 | c.723C>T | p.His241His | synonymous_variant | Exon 10 of 10 | NP_079117.3 | ||
PRR5L | NM_001160168.2 | c.339C>T | p.His113His | synonymous_variant | Exon 6 of 6 | NP_001153640.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.