9-128705522-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013355.5(PKN3):c.244G>A(p.Gly82Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000186 in 1,556,688 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013355.5 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 |
---|---|---|---|---|---|---|---|
PKN3 | NM_013355.5 | c.244G>A | p.Gly82Ser | missense_variant | 2/22 | ENST00000291906.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKN3 | ENST00000291906.5 | c.244G>A | p.Gly82Ser | missense_variant | 2/22 | 1 | NM_013355.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000287 AC: 44AN: 153462Hom.: 0 AF XY: 0.000396 AC XY: 33AN XY: 83404
GnomAD4 exome AF: 0.000192 AC: 270AN: 1404378Hom.: 1 Cov.: 32 AF XY: 0.000226 AC XY: 157AN XY: 693650
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152310Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.244G>A (p.G82S) alteration is located in exon 2 (coding exon 2) of the PKN3 gene. This alteration results from a G to A substitution at nucleotide position 244, causing the glycine (G) at amino acid position 82 to be replaced by a serine (S). 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