10-132404703-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138499.4(PWWP2B):c.203G>A(p.Arg68Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000707 in 1,612,072 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138499.4 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 | UniProt |
---|---|---|---|---|---|---|---|
PWWP2B | NM_138499.4 | c.203G>A | p.Arg68Gln | missense_variant | 2/3 | ENST00000305233.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PWWP2B | ENST00000305233.6 | c.203G>A | p.Arg68Gln | missense_variant | 2/3 | 1 | NM_138499.4 | P1 | |
PWWP2B | ENST00000631148.2 | c.203G>A | p.Arg68Gln | missense_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152026Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000609 AC: 15AN: 246456Hom.: 0 AF XY: 0.0000745 AC XY: 10AN XY: 134272
GnomAD4 exome AF: 0.0000753 AC: 110AN: 1460046Hom.: 1 Cov.: 33 AF XY: 0.0000895 AC XY: 65AN XY: 726324
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152026Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74242
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2022 | The c.203G>A (p.R68Q) alteration is located in exon 2 (coding exon 2) of the PWWP2B gene. This alteration results from a G to A substitution at nucleotide position 203, causing the arginine (R) at amino acid position 68 to be replaced by a glutamine (Q). 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