Variant rs1132816 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_005028.5(PIP4K2A):c.30T>C(p.Ser10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,608,664 control chromosomes in the GnomAD database, including 62,365 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 0.32 ( 9306 hom., cov: 30)

Exomes 𝑓: 0.26 ( 53059 hom. )

Consequence

PIP4K2A
NM_005028.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Variant links:

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]

PIP4K2A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP7

Synonymous conserved (PhyloP=-1.5 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIP4K2A	NM_005028.5 linkuse as main transcript	c.30T>C	p.Ser10=	synonymous_variant	1/10	ENST00000376573.9
PIP4K2A	XM_006717450.3 linkuse as main transcript	c.30T>C	p.Ser10=	synonymous_variant	1/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIP4K2A	ENST00000376573.9 linkuse as main transcript	c.30T>C	p.Ser10=	synonymous_variant	1/10	1	NM_005028.5	P1	P48426-1

Frequencies

GnomAD3 genomes

AF:

0.321

AC:

48556

AN:

151294

Hom.:

9283

Cov.:

show subpopulations

Gnomad AFR

AF:

0.543

Gnomad AMI

AF:

0.206

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.275

Gnomad FIN

AF:

0.171

Gnomad MID

AF:

0.306

Gnomad NFE

AF:

0.264

Gnomad OTH

AF:

0.293

GnomAD3 exomes

AF:

0.247

AC:

60081

AN:

243608

Hom.:

8722

AF XY:

0.247

AC XY:

32679

AN XY:

132246

show subpopulations

Gnomad AFR exome

AF:

0.559

Gnomad AMR exome

AF:

0.134

Gnomad ASJ exome

AF:

0.196

Gnomad EAS exome

AF:

0.116

Gnomad SAS exome

AF:

0.288

Gnomad FIN exome

AF:

0.187

Gnomad NFE exome

AF:

0.262

Gnomad OTH exome

AF:

0.243

GnomAD4 exome

AF:

0.262

AC:

381471

AN:

1457252

Hom.:

53059

Cov.:

AF XY:

0.261

AC XY:

189544

AN XY:

725108

show subpopulations

Gnomad4 AFR exome

AF:

0.556

Gnomad4 AMR exome

AF:

0.143

Gnomad4 ASJ exome

AF:

0.195

Gnomad4 EAS exome

AF:

0.0767

Gnomad4 SAS exome

AF:

0.283

Gnomad4 FIN exome

AF:

0.190

Gnomad4 NFE exome

AF:

0.267

Gnomad4 OTH exome

AF:

0.267

GnomAD4 genome

AF:

0.321

AC:

48628

AN:

151412

Hom.:

9306

Cov.:

AF XY:

0.312

AC XY:

23095

AN XY:

74014

show subpopulations

Gnomad4 AFR

AF:

0.543

Gnomad4 AMR

AF:

0.206

Gnomad4 ASJ

AF:

0.187

Gnomad4 EAS

AF:

0.102

Gnomad4 SAS

AF:

0.275

Gnomad4 FIN

AF:

0.171

Gnomad4 NFE

AF:

0.264

Gnomad4 OTH

AF:

0.294

Alfa

AF:

0.290

Hom.:

3692

Bravo

AF:

0.333

Asia WGS

AF:

0.221

AC:

770

AN:

3474

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

0.61

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over