8-91032300-A-G

Variant names:

• chr8-91032300-A-G
• rs7846412
• NM_018710.3:c.106+8344T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ENSG00000253358 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PIP4P2	NM_018710.3	c.106+8344T>C		intron_variant	Intron 1 of 6	ENST00000285419.8	NP_061180.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIP4P2	ENST00000285419.8	c.106+8344T>C		intron_variant	Intron 1 of 6	1	NM_018710.3	ENSP00000285419.3

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

African (AFR) AF: 0.229 AC: 9495 AN: 41474

American (AMR) AF: 0.418 AC: 6379 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1908 AN: 3470

East Asian (EAS) AF: 0.328 AC: 1699 AN: 5182

South Asian (SAS) AF: 0.645 AC: 3106 AN: 4814

European-Finnish (FIN) AF: 0.594 AC: 6274 AN: 10554

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41347 AN: 67964

Other (OTH) AF: 0.513 AC: 1084 AN: 2112

Alfa AF: 0.566 Hom.: 104920

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
PhyloP100		0.30
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: rs7846412; hg19: chr8-92044528;