rs10828316

chr10-22549460-A-Cchr10-22549460-A-T

Variant summary

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

The NM_005028.5(PIP4K2A):c.792+1199T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,072 control chromosomes in the GnomAD database, including 5,178 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 0.24 (5178 hom., cov: 30)
• Consequence: PIP4K2A NM_005028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIP4K2A	NM_005028.5	c.792+1199T>G		intron_variant		ENST00000376573.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIP4K2A	ENST00000376573.9	c.792+1199T>G		intron_variant		1	NM_005028.5	P1
PIP4K2A	ENST00000323883.11	c.372+1199T>G		intron_variant		2
PIP4K2A	ENST00000545335.5	c.615+1199T>G		intron_variant		2
PIP4K2A	ENST00000604912.1	c.330+1199T>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36175 AN: 151956 Hom.: 5186 Cov.: 30

Gnomad AFR AF: 0.0957

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.238 AC: 36171 AN: 152072 Hom.: 5178 Cov.: 30 AF XY: 0.234 AC XY: 17367 AN XY: 74312

Gnomad4 AFR AF: 0.0955

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.229

Alfa AF: 0.290 Hom.: 3174

Bravo AF: 0.227

Asia WGS AF: 0.279 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	8.1
Dann	Benign	0.54

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: rs10828316; hg19: chr10-22838389;