rs313543

Positions:

• chr4-25267340-G-A
• chr4-25267340-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.1079-1103G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,230 control chromosomes in the GnomAD database, including 41,806 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 0.73 (41806 hom., cov: 34)
• Consequence: PI4K2B NM_018323.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PI4K2B	NM_018323.4	c.1079-1103G>A		intron_variant		ENST00000264864.8
PI4K2B	XM_005248174.3	c.1064-1103G>A		intron_variant
PI4K2B	XM_005248175.5	c.791-1103G>A		intron_variant
PI4K2B	NR_144633.2	n.1225-1103G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PI4K2B	ENST00000264864.8	c.1079-1103G>A		intron_variant		1	NM_018323.4
PI4K2B	ENST00000512921.4	c.791-1103G>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111241 AN: 152112 Hom.: 41786 Cov.: 34

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.731 AC: 111302 AN: 152230 Hom.: 41806 Cov.: 34 AF XY: 0.730 AC XY: 54315 AN XY: 74430

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.739

Alfa AF: 0.794 Hom.: 80001

Bravo AF: 0.715

Asia WGS AF: 0.559 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.33

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: rs313543; hg19: chr4-25268962;