rs313548

Variant names:

• chr4-25235769-G-A
• rs313548
• NM_018323.4:c.268+1338G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-25235769-G-A
• chr4-25235769-G-C
• chr4-25235769-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018323.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PI4K2B	NM_018323.4	MANE Select	c.268+1338G>A		intron	N/A	NP_060793.2	Q8TCG2
	PI4K2B	NR_144633.2		n.399+1338G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PI4K2B	ENST00000264864.8	TSL:1 MANE Select	c.268+1338G>A		intron	N/A	ENSP00000264864.6	Q8TCG2
	PI4K2B	ENST00000871538.1		c.268+1338G>A		intron	N/A	ENSP00000541597.1
	PI4K2B	ENST00000963199.1		c.268+1338G>A		intron	N/A	ENSP00000633258.1

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

African (AFR) AF: 0.585 AC: 24244 AN: 41472

American (AMR) AF: 0.746 AC: 11406 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2526 AN: 3470

East Asian (EAS) AF: 0.668 AC: 3467 AN: 5190

South Asian (SAS) AF: 0.765 AC: 3695 AN: 4830

European-Finnish (FIN) AF: 0.778 AC: 8222 AN: 10564

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52079 AN: 67994

Other (OTH) AF: 0.730 AC: 1542 AN: 2112

Alfa AF: 0.748 Hom.: 117842

Bravo AF: 0.708

Asia WGS AF: 0.703 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.7
DANN	Benign	0.63
PhyloP100		-0.90
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs313548; hg19: chr4-25237391;