rs2230735
Positions:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_005026.5(PIK3CD):āc.678A>Gā(p.Thr226=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,610,348 control chromosomes in the GnomAD database, including 574 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.037 ( 233 hom., cov: 33)
Exomes š: 0.0075 ( 341 hom. )
Consequence
PIK3CD
NM_005026.5 synonymous
NM_005026.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.09
Genes affected
PIK3CD (HGNC:8977): (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta) Phosphoinositide 3-kinases (PI3Ks) phosphorylate inositol lipids and are involved in the immune response. The protein encoded by this gene is a class I PI3K found primarily in leukocytes. Like other class I PI3Ks (p110-alpha p110-beta, and p110-gamma), the encoded protein binds p85 adapter proteins and GTP-bound RAS. However, unlike the other class I PI3Ks, this protein phosphorylates itself, not p85 protein.[provided by RefSeq, Jul 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 1-9716517-A-G is Benign according to our data. Variant chr1-9716517-A-G is described in ClinVar as [Benign]. Clinvar id is 474033.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-5.09 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3CD | NM_005026.5 | c.678A>G | p.Thr226= | synonymous_variant | 6/24 | ENST00000377346.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3CD | ENST00000377346.9 | c.678A>G | p.Thr226= | synonymous_variant | 6/24 | 1 | NM_005026.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0366 AC: 5577AN: 152170Hom.: 230 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
5577
AN:
152170
Hom.:
Cov.:
33
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:
GnomAD3 exomes AF: 0.0182 AC: 4479AN: 246058Hom.: 121 AF XY: 0.0151 AC XY: 2020AN XY: 134148
GnomAD3 exomes
AF:
AC:
4479
AN:
246058
Hom.:
AF XY:
AC XY:
2020
AN XY:
134148
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00753 AC: 10982AN: 1458060Hom.: 341 Cov.: 33 AF XY: 0.00710 AC XY: 5148AN XY: 725350
GnomAD4 exome
AF:
AC:
10982
AN:
1458060
Hom.:
Cov.:
33
AF XY:
AC XY:
5148
AN XY:
725350
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0367 AC: 5596AN: 152288Hom.: 233 Cov.: 33 AF XY: 0.0381 AC XY: 2835AN XY: 74460
GnomAD4 genome
?
AF:
AC:
5596
AN:
152288
Hom.:
Cov.:
33
AF XY:
AC XY:
2835
AN XY:
74460
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
99
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Immunodeficiency 14 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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