rs3215826

Variant names:

• chr10-22536358-AG-A
• rs3215826
• NM_005028.5:c.*842delC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_005028.5(PIP4K2A):​c.*842delC 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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005028.5. 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
	PIP4K2A	NM_005028.5	MANE Select	c.*842delC		3_prime_UTR	Exon 10 of 10	NP_005019.2
	PIP4K2A	NM_001330062.2		c.*842delC		3_prime_UTR	Exon 10 of 10	NP_001316991.1	P48426-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIP4K2A	ENST00000376573.9	TSL:1 MANE Select	c.*842delC		3_prime_UTR	Exon 10 of 10	ENSP00000365757.4	P48426-1
	PIP4K2A	ENST00000899822.1		c.*842delC		3_prime_UTR	Exon 9 of 9	ENSP00000569881.1
	PIP4K2A	ENST00000928212.1		c.*842delC		3_prime_UTR	Exon 8 of 8	ENSP00000598271.1

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

African (AFR) AF: 0.650 AC: 4289 AN: 6596

American (AMR) AF: 0.766 AC: 4712 AN: 6148

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 4987 AN: 8398

East Asian (EAS) AF: 0.641 AC: 13305 AN: 20766

South Asian (SAS) AF: 0.755 AC: 1407 AN: 1864

European-Finnish (FIN) AF: 0.631 AC: 10553 AN: 16730

Middle Eastern (MID) AF: 0.731 AC: 829 AN: 1134

European-Non Finnish (NFE) AF: 0.636 AC: 87222 AN: 137210

Other (OTH) AF: 0.643 AC: 9248 AN: 14392

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

African (AFR) AF: 0.666 AC: 27559 AN: 41376

American (AMR) AF: 0.755 AC: 11526 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2048 AN: 3468

East Asian (EAS) AF: 0.627 AC: 3218 AN: 5130

South Asian (SAS) AF: 0.759 AC: 3648 AN: 4806

European-Finnish (FIN) AF: 0.642 AC: 6741 AN: 10506

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.634 AC: 43050 AN: 67936

Other (OTH) AF: 0.676 AC: 1426 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.39
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3215826;

hg19: chr10-22825287;

COSMIC: COSV60539753;

COSMIC: COSV60539753;