4-25162050-A-G

Variant names:

• chr4-25162050-A-G
• rs11937742
• ENST00000512921.4:c.-21+1297A>G

Variant summary

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

The ENST00000512921.4(PI4K2B):​c.-21+1297A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,082 control chromosomes in the GnomAD database, including 20,047 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 0.50 (20047 hom., cov: 33)
• Consequence: PI4K2B ENST00000512921.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600
• Publications: 5 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]

SEPSECS-AS1 (HGNC:27737): (SEPSECS antisense RNA 1 (head to head))

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512921.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEPSECS-DT	NR_037934.1		n.82+1297A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PI4K2B	ENST00000512921.4	TSL:2	c.-21+1297A>G		intron	N/A	ENSP00000423373.1
	SEPSECS-AS1	ENST00000507794.2	TSL:2	n.82+1297A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76457 AN: 151964 Hom.: 20055 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.503 AC: 76480 AN: 152082 Hom.: 20047 Cov.: 33 AF XY: 0.503 AC XY: 37404 AN XY: 74370

African (AFR) AF: 0.397 AC: 16453 AN: 41460

American (AMR) AF: 0.485 AC: 7410 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1490 AN: 3468

East Asian (EAS) AF: 0.288 AC: 1494 AN: 5182

South Asian (SAS) AF: 0.412 AC: 1989 AN: 4822

European-Finnish (FIN) AF: 0.688 AC: 7259 AN: 10556

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38660 AN: 67986

Other (OTH) AF: 0.504 AC: 1065 AN: 2114

Alfa AF: 0.536 Hom.: 69317

Bravo AF: 0.486

Asia WGS AF: 0.378 AC: 1314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.4
DANN	Benign	0.88
PhyloP100		-0.060
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11937742; hg19: chr4-25163672;