rs10781329

Positions:

• chr9-69003329-G-A

Variant summary

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

The NM_003558.4(PIP5K1B):​c.1621-5118G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,990 control chromosomes in the GnomAD database, including 5,399 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 0.25 (5399 hom., cov: 30)
• Consequence: PIP5K1B NM_003558.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIP5K1B	NM_003558.4	c.1621-5118G>A		intron_variant		ENST00000265382.8	NP_003549.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIP5K1B	ENST00000265382.8	c.1621-5118G>A		intron_variant		1	NM_003558.4	ENSP00000265382.2
PIP5K1B	ENST00000478500.3	n.*614-5118G>A		intron_variant		1		ENSP00000435778.1
PIP5K1B	ENST00000541509.5	c.1503-5118G>A		intron_variant		2		ENSP00000438082.1

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38472 AN: 151872 Hom.: 5397 Cov.: 30

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.253 AC: 38470 AN: 151990 Hom.: 5399 Cov.: 30 AF XY: 0.253 AC XY: 18775 AN XY: 74276

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.287

Alfa AF: 0.298 Hom.: 9838

Bravo AF: 0.245

Asia WGS AF: 0.281 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.61

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: rs10781329; hg19: chr9-71618245;