chr3-139020271-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001013650.2(PRR23B):c.391G>C(p.Val131Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0011 in 1,614,078 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001013650.2 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 |
---|---|---|---|---|---|---|---|
PRR23B | NM_001013650.2 | c.391G>C | p.Val131Leu | missense_variant | 1/1 | ENST00000329447.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRR23B | ENST00000329447.5 | c.391G>C | p.Val131Leu | missense_variant | 1/1 | NM_001013650.2 | P1 | ||
MRPS22 | ENST00000495075.5 | c.-143+14176C>G | intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000467 AC: 71AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000589 AC: 148AN: 251332Hom.: 1 AF XY: 0.000596 AC XY: 81AN XY: 135890
GnomAD4 exome AF: 0.00117 AC: 1709AN: 1461884Hom.: 1 Cov.: 31 AF XY: 0.00110 AC XY: 803AN XY: 727246
GnomAD4 genome ? AF: 0.000467 AC: 71AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74410
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 21, 2021 | 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