rs3747636
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001377334.1(PIK3C2B):āc.3594T>Cā(p.Asn1198=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 1,613,574 control chromosomes in the GnomAD database, including 58,155 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.33 ( 9186 hom., cov: 33)
Exomes š: 0.25 ( 48969 hom. )
Consequence
PIK3C2B
NM_001377334.1 synonymous
NM_001377334.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.980
Genes affected
PIK3C2B (HGNC:8972): (phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta) The protein encoded by this gene belongs to the phosphoinositide 3-kinase (PI3K) family. PI3-kinases play roles in signaling pathways involved in cell proliferation, oncogenic transformation, cell survival, cell migration, and intracellular protein trafficking. This protein contains a lipid kinase catalytic domain as well as a C-terminal C2 domain, a characteristic of class II PI3-kinases. C2 domains act as calcium-dependent phospholipid binding motifs that mediate translocation of proteins to membranes, and may also mediate protein-protein interactions. The PI3-kinase activity of this protein is sensitive to low nanomolar levels of the inhibitor wortmanin. The C2 domain of this protein was shown to bind phospholipids but not Ca2+, which suggests that this enzyme may function in a calcium-independent manner. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP7
Synonymous conserved (PhyloP=-0.98 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3C2B | NM_001377334.1 | c.3594T>C | p.Asn1198= | synonymous_variant | 24/33 | ENST00000684373.1 | |
PIK3C2B | NM_002646.4 | c.3594T>C | p.Asn1198= | synonymous_variant | 26/35 | ||
PIK3C2B | NM_001377335.1 | c.3510T>C | p.Asn1170= | synonymous_variant | 27/36 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3C2B | ENST00000684373.1 | c.3594T>C | p.Asn1198= | synonymous_variant | 24/33 | NM_001377334.1 | P1 | ||
PPP1R15B-AS1 | ENST00000443515.1 | n.147-806A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.326 AC: 49499AN: 152050Hom.: 9168 Cov.: 33
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GnomAD3 exomes AF: 0.296 AC: 74261AN: 250724Hom.: 12280 AF XY: 0.294 AC XY: 39833AN XY: 135518
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GnomAD4 exome AF: 0.247 AC: 361456AN: 1461402Hom.: 48969 Cov.: 34 AF XY: 0.250 AC XY: 181938AN XY: 726992
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GnomAD4 genome AF: 0.326 AC: 49562AN: 152172Hom.: 9186 Cov.: 33 AF XY: 0.332 AC XY: 24710AN XY: 74384
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at