10-22544134-A-T

Variant names:

• chr10-22544134-A-T
• rs10430590
• NM_005028.5:c.793-2087T>A

Variant summary

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

The NM_005028.5(PIP4K2A):​c.793-2087T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,058 control chromosomes in the GnomAD database, including 4,863 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 0.22 (4863 hom., cov: 31)
• Consequence: PIP4K2A NM_005028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIP4K2A	NM_005028.5	c.793-2087T>A		intron_variant	Intron 7 of 9	ENST00000376573.9	NP_005019.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIP4K2A	ENST00000376573.9	c.793-2087T>A		intron_variant	Intron 7 of 9	1	NM_005028.5	ENSP00000365757.4
PIP4K2A	ENST00000545335.5	c.616-2087T>A		intron_variant	Intron 7 of 9	2		ENSP00000442098.1
PIP4K2A	ENST00000323883.11	c.373-2087T>A		intron_variant	Intron 5 of 7	2		ENSP00000326294.7
PIP4K2A	ENST00000604912.1	c.331-2087T>A		intron_variant	Intron 4 of 4	2		ENSP00000473858.1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34213 AN: 151940 Hom.: 4869 Cov.: 31

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.225 AC: 34205 AN: 152058 Hom.: 4863 Cov.: 31 AF XY: 0.222 AC XY: 16475 AN XY: 74316

African (AFR) AF: 0.0671 AC: 2785 AN: 41508

American (AMR) AF: 0.163 AC: 2494 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1052 AN: 3468

East Asian (EAS) AF: 0.408 AC: 2102 AN: 5148

South Asian (SAS) AF: 0.186 AC: 896 AN: 4824

European-Finnish (FIN) AF: 0.307 AC: 3248 AN: 10566

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.303 AC: 20603 AN: 67952

Other (OTH) AF: 0.217 AC: 459 AN: 2112

Alfa AF: 0.257 Hom.: 715

Bravo AF: 0.212

Asia WGS AF: 0.273 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.57
PhyloP100		0.34
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10430590; hg19: chr10-22833063;