3-139020309-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001013650.2(PRR23B):c.353C>T(p.Ser118Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,613,974 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001013650.2 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRR23B | NM_001013650.2 | c.353C>T | p.Ser118Leu | missense_variant | 1/1 | ENST00000329447.5 | NP_001013672.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRR23B | ENST00000329447.5 | c.353C>T | p.Ser118Leu | missense_variant | 1/1 | 6 | NM_001013650.2 | ENSP00000328768.5 | ||
MRPS22 | ENST00000495075.5 | c.-143+14214G>A | intron_variant | 1 | ENSP00000418008.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251240Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135876
GnomAD4 exome AF: 0.000150 AC: 220AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.000157 AC XY: 114AN XY: 727240
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152096Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2022 | The c.353C>T (p.S118L) alteration is located in exon 1 (coding exon 1) of the PRR23B gene. This alteration results from a C to T substitution at nucleotide position 353, causing the serine (S) at amino acid position 118 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