12-18282440-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001288772.2(PIK3C2G):c.359C>A(p.Thr120Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,609,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001288772.2 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 |
---|---|---|---|---|---|---|---|---|
PIK3C2G | NM_001288772.2 | c.359C>A | p.Thr120Lys | missense_variant | 2/33 | ENST00000538779.6 | NP_001275701.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIK3C2G | ENST00000538779.6 | c.359C>A | p.Thr120Lys | missense_variant | 2/33 | 5 | NM_001288772.2 | ENSP00000445381.1 |
Frequencies
GnomAD3 genomes AF: 0.000108 AC: 16AN: 148592Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000523 AC: 13AN: 248716Hom.: 0 AF XY: 0.0000519 AC XY: 7AN XY: 134964
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1460876Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 726776
GnomAD4 genome AF: 0.000114 AC: 17AN: 148708Hom.: 0 Cov.: 32 AF XY: 0.000165 AC XY: 12AN XY: 72542
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2024 | The c.359C>A (p.T120K) alteration is located in exon 2 (coding exon 1) of the PIK3C2G gene. This alteration results from a C to A substitution at nucleotide position 359, causing the threonine (T) at amino acid position 120 to be replaced by a lysine (K). 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