Variant rs1053454 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005028.5(PIP4K2A):c.*37T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 1,526,178 control chromosomes in the GnomAD database, including 326,757 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 0.71 ( 38556 hom., cov: 29)

Exomes 𝑓: 0.64 ( 288201 hom. )

Consequence

PIP4K2A
NM_005028.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.88

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:

PIP4K2A (HGNC:):

PIP4K2A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIP4K2A	NM_005028.5 linkuse as main transcript	c.*37T>G		3_prime_UTR_variant	10/10	ENST00000376573.9	NP_005019.2	P48426-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PIP4K2A	ENST00000376573 linkuse as main transcript	c.*37T>G	3_prime_UTR_variant	10/10	1	NM_005028.5	ENSP00000365757.4	P48426-1
PIP4K2A	ENST00000545335 linkuse as main transcript	c.*37T>G	3_prime_UTR_variant	10/10	2		ENSP00000442098.1	P48426-2
PIP4K2A	ENST00000323883 linkuse as main transcript	c.*37T>G	3_prime_UTR_variant	8/8	2		ENSP00000326294.7	H7BXS3
PIP4K2A	ENST00000474335.1 linkuse as main transcript	n.288T>G	non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.707

AC:

107143

AN:

151612

Hom.:

38511

Cov.:

show subpopulations

Gnomad AFR

AF:

0.831

Gnomad AMI

AF:

0.401

Gnomad AMR

AF:

0.778

Gnomad ASJ

AF:

0.591

Gnomad EAS

AF:

0.631

Gnomad SAS

AF:

0.779

Gnomad FIN

AF:

0.642

Gnomad MID

AF:

0.771

Gnomad NFE

AF:

0.635

Gnomad OTH

AF:

0.716

GnomAD3 exomes

AF:

0.692

AC:

137999

AN:

199472

Hom.:

48413

AF XY:

0.690

AC XY:

73562

AN XY:

106626

show subpopulations

Gnomad AFR exome

AF:

0.840

Gnomad AMR exome

AF:

0.825

Gnomad ASJ exome

AF:

0.596

Gnomad EAS exome

AF:

0.622

Gnomad SAS exome

AF:

0.770

Gnomad FIN exome

AF:

0.635

Gnomad NFE exome

AF:

0.635

Gnomad OTH exome

AF:

0.677

GnomAD4 exome

AF:

0.644

AC:

885794

AN:

1374446

Hom.:

288201

Cov.:

AF XY:

0.647

AC XY:

442368

AN XY:

683738

show subpopulations

Gnomad4 AFR exome

AF:

0.835

Gnomad4 AMR exome

AF:

0.817

Gnomad4 ASJ exome

AF:

0.594

Gnomad4 EAS exome

AF:

0.632

Gnomad4 SAS exome

AF:

0.769

Gnomad4 FIN exome

AF:

0.632

Gnomad4 NFE exome

AF:

0.623

Gnomad4 OTH exome

AF:

0.655

GnomAD4 genome

AF:

0.707

AC:

107255

AN:

151732

Hom.:

38556

Cov.:

AF XY:

0.713

AC XY:

52807

AN XY:

74114

show subpopulations

Gnomad4 AFR

AF:

0.831

Gnomad4 AMR

AF:

0.778

Gnomad4 ASJ

AF:

0.591

Gnomad4 EAS

AF:

0.632

Gnomad4 SAS

AF:

0.779

Gnomad4 FIN

AF:

0.642

Gnomad4 NFE

AF:

0.635

Gnomad4 OTH

AF:

0.715

Alfa

AF:

0.660

Hom.:

34482

Bravo

AF:

0.716

Asia WGS

AF:

0.711

AC:

2470

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

9.4

DANN

Benign

0.54

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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