rs7846412

Positions:

• chr8-91032300-A-G
• chr8-91032300-A-T

Variant summary

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

The NM_018710.3(PIP4P2):​c.106+8344T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,048 control chromosomes in the GnomAD database, including 19,288 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 0.47 (19288 hom., cov: 32)
• Consequence: PIP4P2 NM_018710.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301

Genes affected

PIP4P2 (HGNC:25452): (phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2) TMEM55A catalyzes the degradation of phosphatidylinositol 4,5-bisphosphate (PtdIns-4,5-P2) by removing the 4-phosphate (Ungewickell et al., 2005 [PubMed 16365287]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIP4P2	NM_018710.3	c.106+8344T>C		intron_variant		ENST00000285419.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIP4P2	ENST00000285419.8	c.106+8344T>C		intron_variant		1	NM_018710.3	P1

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72047 AN: 151928 Hom.: 19287 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.474 AC: 72048 AN: 152048 Hom.: 19288 Cov.: 32 AF XY: 0.475 AC XY: 35290 AN XY: 74342

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.513

Alfa AF: 0.579 Hom.: 52536

Bravo AF: 0.444

Asia WGS AF: 0.498 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	9.2
DANN	Benign	0.91

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: rs7846412; hg19: chr8-92044528;