rs3215826

Positions:

• chr10-22536358-AG-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_005028.5(PIP4K2A):​c.*842del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.66 (32910 hom., cov: 0)
  • Exomes 𝑓: 0.64 (44062 hom.)
• Consequence: PIP4K2A NM_005028.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394

Genes affected

PIP4K2A (HGNC:8997): (phosphatidylinositol-5-phosphate 4-kinase type 2 alpha) Phosphatidylinositol-5,4-bisphosphate, the precursor to second messengers of the phosphoinositide signal transduction pathways, is thought to be involved in the regulation of secretion, cell proliferation, differentiation, and motility. The protein encoded by this gene is one of a family of enzymes capable of catalyzing the phosphorylation of phosphatidylinositol-5-phosphate on the fourth hydroxyl of the myo-inositol ring to form phosphatidylinositol-5,4-bisphosphate. The amino acid sequence of this enzyme does not show homology to other kinases, but the recombinant protein does exhibit kinase activity. This gene is a member of the phosphatidylinositol-5-phosphate 4-kinase family. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIP4K2A	NM_005028.5	c.*842del		3_prime_UTR_variant	10/10	ENST00000376573.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIP4K2A	ENST00000376573.9	c.*842del		3_prime_UTR_variant	10/10	1	NM_005028.5	P1

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99725 AN: 151676 Hom.: 32883 Cov.: 0

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.677

GnomAD4 exome AF: 0.640 AC: 136552 AN: 213238 Hom.: 44062 Cov.: 0 AF XY: 0.640 AC XY: 68686 AN XY: 107290

Gnomad4 AFR exome AF: 0.650

Gnomad4 AMR exome AF: 0.766

Gnomad4 ASJ exome AF: 0.594

Gnomad4 EAS exome AF: 0.641

Gnomad4 SAS exome AF: 0.755

Gnomad4 FIN exome AF: 0.631

Gnomad4 NFE exome AF: 0.636

Gnomad4 OTH exome AF: 0.643

GnomAD4 genome AF: 0.658 AC: 99807 AN: 151796 Hom.: 32910 Cov.: 0 AF XY: 0.665 AC XY: 49311 AN XY: 74148

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.676

Alfa AF: 0.651 Hom.: 3915

Bravo AF: 0.659

Asia WGS AF: 0.689 AC: 2395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs3215826; hg19: chr10-22825287;