chr1-46043848-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_003629.4(PIK3R3):c.1211G>A(p.Cys404Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,724 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 (★).
Frequency
Consequence
NM_003629.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIK3R3 | ENST00000262741.10 | c.1211G>A | p.Cys404Tyr | missense_variant | Exon 10 of 10 | 1 | NM_003629.4 | ENSP00000262741.5 | ||
P3R3URF-PIK3R3 | ENST00000540385.2 | c.1349G>A | p.Cys450Tyr | missense_variant | Exon 10 of 10 | 2 | ENSP00000439913.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461538Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727050
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1211G>A (p.C404Y) alteration is located in exon 10 (coding exon 10) of the PIK3R3 gene. This alteration results from a G to A substitution at nucleotide position 1211, causing the cysteine (C) at amino acid position 404 to be replaced by a tyrosine (Y). 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