rs1043515

chr17-38765943-A-G

Variant summary

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

The NM_003559.5(PIP4K2B):c.*3748T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 152,510 control chromosomes in the GnomAD database, including 17,456 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 0.46 (17381 hom., cov: 32)
  • Exomes 𝑓: 0.56 (75 hom.)
• Consequence: PIP4K2B NM_003559.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

Genes affected

PIP4K2B (HGNC:8998): (phosphatidylinositol-5-phosphate 4-kinase type 2 beta) The protein encoded by this gene catalyzes the phosphorylation of phosphatidylinositol-5-phosphate on the fourth hydroxyl of the myo-inositol ring to form phosphatidylinositol-5,4-bisphosphate. This gene is a member of the phosphatidylinositol-5-phosphate 4-kinase family. The encoded protein sequence does not show similarity to other kinases, but the protein does exhibit kinase activity. Additionally, the encoded protein interacts with p55 TNF receptor. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIP4K2B	NM_003559.5	c.*3748T>C		3_prime_UTR_variant	10/10	ENST00000619039.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIP4K2B	ENST00000619039.5	c.*3748T>C		3_prime_UTR_variant	10/10	1	NM_003559.5	P1

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70429 AN: 151938 Hom.: 17375 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.496

GnomAD4 exome AF: 0.559 AC: 254 AN: 454 Hom.: 75 Cov.: 0 AF XY: 0.529 AC XY: 146 AN XY: 276

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.552

Gnomad4 NFE exome AF: 0.682

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.463 AC: 70442 AN: 152056 Hom.: 17381 Cov.: 32 AF XY: 0.460 AC XY: 34216 AN XY: 74334

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.497

Alfa AF: 0.537 Hom.: 29389

Bravo AF: 0.449

Asia WGS AF: 0.345 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	5.7
Dann	Benign	0.79

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: rs1043515; hg19: chr17-36922196;