3-23917960-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_002948.5(RPL15):c.101C>T(p.Ser34Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,744 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_002948.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPL15 | NM_002948.5 | c.101C>T | p.Ser34Phe | missense_variant | Exon 2 of 4 | ENST00000307839.10 | NP_002939.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152262Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249354Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135394
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461482Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727044
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
DNA sequence analysis of the RPL15 gene demonstrated a sequence change, c.101C>T, in exon 2 that results in an amino acid change, p.Ser34Phe. This sequence change has been described in the gnomAD database in two individuals which corresponds to a population frequency of 0.0007% (dbSNP rs766367909). The p.Ser34Phe change affects a highly conserved amino acid residue located in a domain of the RPL15 protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Ser34Phe substitution. This sequence change does not appear to have been previously described in individuals with RPL15-related disorders. Due to insufficient evidences and the lack of functional studies, the clinical significance of the p.Ser34Phe change remains unknown at this time. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at