chr11-17089725-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002645.4(PIK3C2A):c.*13T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 1,585,344 control chromosomes in the GnomAD database, including 241,812 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.58 ( 25813 hom., cov: 32)
Exomes 𝑓: 0.54 ( 215999 hom. )
Consequence
PIK3C2A
NM_002645.4 3_prime_UTR
NM_002645.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.820
Genes affected
PIK3C2A (HGNC:8971): (phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha) 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 not sensitive to nanomolar levels of the inhibitor wortmanin. This protein was shown to be able to be activated by insulin and may be involved in integrin-dependent signaling. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 11-17089725-A-G is Benign according to our data. Variant chr11-17089725-A-G is described in ClinVar as [Benign]. Clinvar id is 1327026.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3C2A | NM_002645.4 | c.*13T>C | 3_prime_UTR_variant | 33/33 | ENST00000691414.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3C2A | ENST00000691414.1 | c.*13T>C | 3_prime_UTR_variant | 33/33 | NM_002645.4 | P1 | |||
PIK3C2A | ENST00000265970.11 | c.*13T>C | 3_prime_UTR_variant | 32/32 | 1 | P1 | |||
PIK3C2A | ENST00000531428.1 | n.1400+1609T>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.579 AC: 87888AN: 151858Hom.: 25770 Cov.: 32
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GnomAD3 exomes AF: 0.590 AC: 146465AN: 248242Hom.: 44134 AF XY: 0.587 AC XY: 78827AN XY: 134204
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GnomAD4 exome AF: 0.544 AC: 780043AN: 1433368Hom.: 215999 Cov.: 25 AF XY: 0.546 AC XY: 390012AN XY: 713838
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GnomAD4 genome ? AF: 0.579 AC: 87992AN: 151976Hom.: 25813 Cov.: 32 AF XY: 0.580 AC XY: 43114AN XY: 74284
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Oculocerebrodental syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at