rs2881900

chr3-138830167-A-G

Variant summary

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

The NM_006219.3(PIK3CB):c.-122+4528T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,904 control chromosomes in the GnomAD database, including 22,236 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 0.51 (22236 hom., cov: 31)
• Consequence: PIK3CB NM_006219.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3CB	NM_006219.3	c.-122+4528T>C		intron_variant		ENST00000674063.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3CB	ENST00000674063.1	c.-122+4528T>C		intron_variant			NM_006219.3	P1
PIK3CB	ENST00000477593.5	c.-17+4528T>C		intron_variant		5		P1
PIK3CB	ENST00000483968.5	c.-189+4528T>C		intron_variant		3
PIK3CB	ENST00000462898.5	c.-17+4528T>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77333 AN: 151786 Hom.: 22203 Cov.: 31

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.510 AC: 77412 AN: 151904 Hom.: 22236 Cov.: 31 AF XY: 0.494 AC XY: 36680 AN XY: 74248

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.0149

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.504

Alfa AF: 0.487 Hom.: 2423

Bravo AF: 0.522

Asia WGS AF: 0.205 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.85
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2881900; hg19: chr3-138549009;