18-41970335-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_002647.4(PIK3C3):c.410G>A(p.Arg137His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000812 in 1,612,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R137C) has been classified as Uncertain significance.
Frequency
Consequence
NM_002647.4 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 |
---|---|---|---|---|---|---|---|
PIK3C3 | NM_002647.4 | c.410G>A | p.Arg137His | missense_variant | 4/25 | ENST00000262039.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3C3 | ENST00000262039.9 | c.410G>A | p.Arg137His | missense_variant | 4/25 | 1 | NM_002647.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151866Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251050Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135692
GnomAD4 exome AF: 0.0000862 AC: 126AN: 1461006Hom.: 0 Cov.: 30 AF XY: 0.0000880 AC XY: 64AN XY: 726878
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151866Hom.: 0 Cov.: 32 AF XY: 0.0000540 AC XY: 4AN XY: 74120
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | PIK3C3: PM2, PP3 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at