rs10511961

Positions:

• chr9-68882569-G-C
• chr9-68882569-G-T

Variant summary

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

The NM_003558.4(PIP5K1B):​c.318+5775G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,906 control chromosomes in the GnomAD database, including 11,912 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 0.38 (11912 hom., cov: 32)
• Consequence: PIP5K1B NM_003558.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

Genes affected

PIP5K1B (HGNC:8995): (phosphatidylinositol-4-phosphate 5-kinase type 1 beta) Predicted to enable 1-phosphatidylinositol-4-phosphate 5-kinase activity. Predicted to be involved in regulation of phosphatidylinositol 3-kinase signaling. Predicted to act upstream of or within phosphatidylinositol biosynthetic process. Located in uropod. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIP5K1B	NM_003558.4	c.318+5775G>C		intron_variant		ENST00000265382.8	NP_003549.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIP5K1B	ENST00000265382.8	c.318+5775G>C		intron_variant		1	NM_003558.4	ENSP00000265382	P1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57698 AN: 151788 Hom.: 11910 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.380 AC: 57710 AN: 151906 Hom.: 11912 Cov.: 32 AF XY: 0.379 AC XY: 28155 AN XY: 74234

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.390

Alfa AF: 0.282 Hom.: 768

Bravo AF: 0.370

Asia WGS AF: 0.273 AC: 952 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	13
DANN	Benign	0.63

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: rs10511961; hg19: chr9-71497485; COSMIC: COSV55244505;