chr3-138666573-C-T

Position:

• chr3-138666573-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006219.3(PIK3CB):​c.2505-1370G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,012 control chromosomes in the GnomAD database, including 12,252 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 0.36 (12252 hom., cov: 32)
• Consequence: PIK3CB NM_006219.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

Genes affected

PIK3CB (HGNC:8976): (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) This gene encodes an isoform of the catalytic subunit of phosphoinositide 3-kinase (PI3K). These kinases are important in signaling pathways involving receptors on the outer membrane of eukaryotic cells and are named for their catalytic subunit. The encoded protein is the catalytic subunit for PI3Kbeta (PI3KB). PI3KB has been shown to be part of the activation pathway in neutrophils which have bound immune complexes at sites of injury or infection. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2011]

PIK3CB (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIK3CB	NM_006219.3	c.2505-1370G>A		intron_variant		ENST00000674063.1	NP_006210.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIK3CB	ENST00000674063.1	c.2505-1370G>A		intron_variant			NM_006219.3	ENSP00000501150.1

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54541 AN: 151894 Hom.: 12240 Cov.: 32

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.373

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.359 AC: 54566 AN: 152012 Hom.: 12252 Cov.: 32 AF XY: 0.365 AC XY: 27113 AN XY: 74290

Gnomad4 AFR AF: 0.0860

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.372

Alfa AF: 0.408 Hom.: 7045

Bravo AF: 0.355

Asia WGS AF: 0.450 AC: 1561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.43

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

Other links and lift over

dbSNP: rs9878820; hg19: chr3-138385415;