17-38850437-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_000978.4(RPL23):c.265C>G(p.Arg89Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,684 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R89H) has been classified as Uncertain significance.
Frequency
Consequence
NM_000978.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL23 | NM_000978.4 | c.265C>G | p.Arg89Gly | missense_variant | 4/5 | ENST00000479035.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL23 | ENST00000479035.7 | c.265C>G | p.Arg89Gly | missense_variant | 4/5 | 1 | NM_000978.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152018Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251416Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135880
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461666Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727158
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152018Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5AN XY: 74222
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Apr 14, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant  is likely to be tolerated. This variant has not been reported in the literature in individuals affected with RPL23-related conditions. This variant is present in population databases (rs770495795, gnomAD 0.02%). This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 89 of the RPL23 protein (p.Arg89Gly). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at