rs1556751

chr9-68818296-G-Achr9-68818296-G-Cchr9-68818296-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.-85-165G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,132 control chromosomes in the GnomAD database, including 30,749 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 0.63 (30749 hom., cov: 33)
• Consequence: PIP5K1B NM_003558.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIP5K1B	NM_003558.4	c.-85-165G>A		intron_variant		ENST00000265382.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIP5K1B	ENST00000265382.8	c.-85-165G>A		intron_variant		1	NM_003558.4	P1

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96357 AN: 152014 Hom.: 30733 Cov.: 33

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.634 AC: 96424 AN: 152132 Hom.: 30749 Cov.: 33 AF XY: 0.638 AC XY: 47454 AN XY: 74346

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.626

Alfa AF: 0.628 Hom.: 60498

Bravo AF: 0.637

Asia WGS AF: 0.679 AC: 2362 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	0.85
Dann	Benign	0.19

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: rs1556751; hg19: chr9-71433212;