3-138795819-C-T

Variant names:

• chr3-138795819-C-T
• rs9834963
• NM_006219.3:c.-17+644G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006219.3(PIK3CB):​c.-17+644G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,908 control chromosomes in the GnomAD database, including 27,796 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 0.60 (27796 hom., cov: 30)
• Consequence: PIK3CB NM_006219.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIK3CB	NM_006219.3	c.-17+644G>A		intron_variant	Intron 2 of 23	ENST00000674063.1	NP_006210.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIK3CB	ENST00000674063.1	c.-17+644G>A		intron_variant	Intron 2 of 23		NM_006219.3	ENSP00000501150.1
PIK3CB	ENST00000477593.6	c.-16-36460G>A		intron_variant	Intron 1 of 22	5		ENSP00000418143.1
PIK3CB	ENST00000483968.5	c.-84+644G>A		intron_variant	Intron 2 of 4	3		ENSP00000419857.1
PIK3CB	ENST00000462898.5	n.-16-36460G>A		intron_variant	Intron 1 of 22	5		ENSP00000420108.1

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90389 AN: 151790 Hom.: 27752 Cov.: 30

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.596 AC: 90489 AN: 151908 Hom.: 27796 Cov.: 30 AF XY: 0.607 AC XY: 45023 AN XY: 74228

African (AFR) AF: 0.613 AC: 25370 AN: 41398

American (AMR) AF: 0.663 AC: 10100 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1671 AN: 3470

East Asian (EAS) AF: 0.985 AC: 5092 AN: 5170

South Asian (SAS) AF: 0.657 AC: 3165 AN: 4816

European-Finnish (FIN) AF: 0.663 AC: 7007 AN: 10566

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36300 AN: 67946

Other (OTH) AF: 0.574 AC: 1213 AN: 2112

Alfa AF: 0.559 Hom.: 6056

Bravo AF: 0.598

Asia WGS AF: 0.820 AC: 2849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.40
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs9834963; hg19: chr3-138514661;