chr12-18282440-C-T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001288772.2(PIK3C2G):c.359C>T(p.Thr120Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000497 in 1,609,468 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T120K) has been classified as Uncertain significance.
Frequency
Consequence
NM_001288772.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000673 AC: 1AN: 148592Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000201 AC: 5AN: 248716 AF XY: 0.0000222 show subpopulations
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460876Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 726778 show subpopulations
GnomAD4 genome AF: 0.00000673 AC: 1AN: 148592Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 1AN XY: 72416 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at