NM_001377334.1:c.3516+1082C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001377334.1(PIK3C2B):c.3516+1082C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0217 in 152,278 control chromosomes in the GnomAD database, including 70 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: 𝑓 0.022 ( 70 hom., cov: 32)
Consequence
PIK3C2B
NM_001377334.1 intron
NM_001377334.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.196
Publications
0 publications found
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIK3C2B | NM_001377334.1 | c.3516+1082C>T | intron_variant | Intron 23 of 32 | ENST00000684373.1 | NP_001364263.1 | ||
PIK3C2B | NM_002646.4 | c.3516+1082C>T | intron_variant | Intron 25 of 34 | NP_002637.3 | |||
PIK3C2B | NM_001377335.1 | c.3432+1082C>T | intron_variant | Intron 26 of 35 | NP_001364264.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0217 AC: 3309AN: 152160Hom.: 70 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
3309
AN:
152160
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0217 AC: 3309AN: 152278Hom.: 70 Cov.: 32 AF XY: 0.0223 AC XY: 1661AN XY: 74452 show subpopulations
GnomAD4 genome
AF:
AC:
3309
AN:
152278
Hom.:
Cov.:
32
AF XY:
AC XY:
1661
AN XY:
74452
show subpopulations
African (AFR)
AF:
AC:
839
AN:
41546
American (AMR)
AF:
AC:
275
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
AC:
61
AN:
3470
East Asian (EAS)
AF:
AC:
658
AN:
5172
South Asian (SAS)
AF:
AC:
254
AN:
4822
European-Finnish (FIN)
AF:
AC:
64
AN:
10624
Middle Eastern (MID)
AF:
AC:
11
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1103
AN:
68032
Other (OTH)
AF:
AC:
44
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
168
336
504
672
840
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
42
84
126
168
210
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
247
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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