1-9690399-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005026.5(PIK3CD):​c.-137-1068T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,134 control chromosomes in the GnomAD database, including 17,750 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 0.48 ( 17750 hom., cov: 32)

Consequence

PIK3CD
NM_005026.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.02
Variant links:
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PIK3CDNM_005026.5 linkc.-137-1068T>C intron_variant ENST00000377346.9 NP_005017.3 O00329-1A0A2K8FKV1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PIK3CDENST00000377346.9 linkc.-137-1068T>C intron_variant 1 NM_005026.5 ENSP00000366563.4 O00329-1

Frequencies

GnomAD3 genomes
AF:
0.484
AC:
73526
AN:
152016
Hom.:
17734
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.478
Gnomad AMI
AF:
0.401
Gnomad AMR
AF:
0.528
Gnomad ASJ
AF:
0.480
Gnomad EAS
AF:
0.459
Gnomad SAS
AF:
0.604
Gnomad FIN
AF:
0.465
Gnomad MID
AF:
0.497
Gnomad NFE
AF:
0.475
Gnomad OTH
AF:
0.481
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.484
AC:
73584
AN:
152134
Hom.:
17750
Cov.:
32
AF XY:
0.487
AC XY:
36190
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.478
Gnomad4 AMR
AF:
0.528
Gnomad4 ASJ
AF:
0.480
Gnomad4 EAS
AF:
0.459
Gnomad4 SAS
AF:
0.604
Gnomad4 FIN
AF:
0.465
Gnomad4 NFE
AF:
0.475
Gnomad4 OTH
AF:
0.482
Alfa
AF:
0.494
Hom.:
9373
Bravo
AF:
0.487
Asia WGS
AF:
0.525
AC:
1822
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
0.27
DANN
Benign
0.79

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4240910; hg19: chr1-9750457; API