9-68818296-G-A

Variant names:

• chr9-68818296-G-A
• rs1556751
• NM_003558.4:c.-85-165G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003558.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIP5K1B	NM_003558.4	MANE Select	c.-85-165G>A		intron	N/A	NP_003549.1
	PIP5K1B	NM_001376036.1		c.-85-165G>A		intron	N/A	NP_001362965.1
	PIP5K1B	NM_001376037.1		c.-85-165G>A		intron	N/A	NP_001362966.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIP5K1B	ENST00000265382.8	TSL:1 MANE Select	c.-85-165G>A		intron	N/A	ENSP00000265382.2
	PIP5K1B	ENST00000478500.3	TSL:1	n.-85-165G>A		intron	N/A	ENSP00000435778.1
	PIP5K1B	ENST00000541509.5	TSL:2	c.-85-165G>A		intron	N/A	ENSP00000438082.1

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

African (AFR) AF: 0.586 AC: 24314 AN: 41482

American (AMR) AF: 0.727 AC: 11111 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2314 AN: 3468

East Asian (EAS) AF: 0.630 AC: 3264 AN: 5182

South Asian (SAS) AF: 0.715 AC: 3449 AN: 4826

European-Finnish (FIN) AF: 0.693 AC: 7331 AN: 10576

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42429 AN: 67986

Other (OTH) AF: 0.626 AC: 1324 AN: 2116

Alfa AF: 0.628 Hom.: 128273

Bravo AF: 0.637

Asia WGS AF: 0.679 AC: 2362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.85
DANN	Benign	0.19
PhyloP100		-0.28
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: rs1556751; hg19: chr9-71433212;