rs313548

chr4-25235769-G-Achr4-25235769-G-Cchr4-25235769-G-T

Variant summary

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

The NM_018323.4(PI4K2B):c.268+1338G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,118 control chromosomes in the GnomAD database, including 38,906 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 0.71 (38906 hom., cov: 32)
• Consequence: PI4K2B NM_018323.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903

Genes affected

PI4K2B (HGNC:18215): (phosphatidylinositol 4-kinase type 2 beta) This gene encodes a member of the type II PI4 kinase protein family. The encoded protein is primarily cytosolic and contributes to overall PI4-kinase activity along with other protein family members. This protein is involved in early T cell activation. [provided by RefSeq, Dec 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PI4K2B	NM_018323.4	c.268+1338G>A		intron_variant		ENST00000264864.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PI4K2B	ENST00000264864.8	c.268+1338G>A		intron_variant		1	NM_018323.4
PI4K2B	ENST00000512921.4	c.-20-16552G>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108156 AN: 152000 Hom.: 38899 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.711 AC: 108198 AN: 152118 Hom.: 38906 Cov.: 32 AF XY: 0.712 AC XY: 52955 AN XY: 74344

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.730

Alfa AF: 0.759 Hom.: 69777

Bravo AF: 0.708

Asia WGS AF: 0.703 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.7
Dann	Benign	0.63

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: rs313548; hg19: chr4-25237391;