rs7088318

Variant names:

• chr10-22564019-C-A
• rs7088318
• NM_005028.5:c.678+3832G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-22564019-C-A
• chr10-22564019-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005028.5(PIP4K2A):​c.678+3832G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,986 control chromosomes in the GnomAD database, including 24,733 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 0.56 (24733 hom., cov: 32)
• Consequence: PIP4K2A NM_005028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 26 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.75 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIP4K2A	NM_005028.5	MANE Select	c.678+3832G>T		intron	N/A	NP_005019.2
	PIP4K2A	NM_001330062.2		c.501+3832G>T		intron	N/A	NP_001316991.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIP4K2A	ENST00000376573.9	TSL:1 MANE Select	c.678+3832G>T		intron	N/A	ENSP00000365757.4
	PIP4K2A	ENST00000545335.5	TSL:2	c.501+3832G>T		intron	N/A	ENSP00000442098.1
	PIP4K2A	ENST00000323883.11	TSL:2	c.258+3832G>T		intron	N/A	ENSP00000326294.7

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85019 AN: 151866 Hom.: 24718 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.560 AC: 85052 AN: 151986 Hom.: 24733 Cov.: 32 AF XY: 0.571 AC XY: 42387 AN XY: 74262

African (AFR) AF: 0.394 AC: 16343 AN: 41442

American (AMR) AF: 0.705 AC: 10764 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3470

East Asian (EAS) AF: 0.584 AC: 3018 AN: 5168

South Asian (SAS) AF: 0.770 AC: 3708 AN: 4814

European-Finnish (FIN) AF: 0.633 AC: 6679 AN: 10548

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40979 AN: 67962

Other (OTH) AF: 0.583 AC: 1230 AN: 2108

Alfa AF: 0.589 Hom.: 91635

Bravo AF: 0.549

Asia WGS AF: 0.659 AC: 2291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.18
DANN	Benign	0.69
PhyloP100		-1.2
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

Other links and lift over

dbSNP: rs7088318; hg19: chr10-22852948;