rs6834255

chr4-25277698-G-Achr4-25277698-G-C

Variant summary

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

The NM_018323.4(PI4K2B):c.*511G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,172 control chromosomes in the GnomAD database, including 2,244 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 0.17 (2244 hom., cov: 33)
  • Exomes 𝑓: 0.24 (0 hom.)
• Consequence: PI4K2B NM_018323.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PI4K2B	NM_018323.4	c.*511G>A		3_prime_UTR_variant	10/10	ENST00000264864.8
PI4K2B	XM_005248174.3	c.*511G>A		3_prime_UTR_variant	10/10
PI4K2B	XM_005248175.5	c.*511G>A		3_prime_UTR_variant	10/10
PI4K2B	NR_144633.2	n.2103G>A		non_coding_transcript_exon_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PI4K2B	ENST00000264864.8	c.*511G>A		3_prime_UTR_variant	10/10	1	NM_018323.4

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25547 AN: 151976 Hom.: 2232 Cov.: 33

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.161

GnomAD4 exome AF: 0.237 AC: 19 AN: 80 Hom.: 0 Cov.: 0 AF XY: 0.182 AC XY: 4 AN XY: 22

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.0833

Gnomad4 NFE exome AF: 0.222

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.168 AC: 25582 AN: 152092 Hom.: 2244 Cov.: 33 AF XY: 0.169 AC XY: 12542 AN XY: 74328

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.163

Alfa AF: 0.161 Hom.: 3392

Bravo AF: 0.169

Asia WGS AF: 0.252 AC: 872 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.1
Dann	Benign	0.50

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: rs6834255; hg19: chr4-25279320;