NM_003558.4:c.-85-4231C>T

Variant names:

• chr9-68814230-C-T
• rs10869335
• NM_003558.4:c.-85-4231C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003558.4(PIP5K1B):​c.-85-4231C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 151,718 control chromosomes in the GnomAD database, including 14,719 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 0.44 (14719 hom., cov: 32)
• Consequence: PIP5K1B NM_003558.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 2 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIP5K1B	NM_003558.4	c.-85-4231C>T		intron_variant	Intron 2 of 15	ENST00000265382.8	NP_003549.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIP5K1B	ENST00000265382.8	c.-85-4231C>T		intron_variant	Intron 2 of 15	1	NM_003558.4	ENSP00000265382.2
PIP5K1B	ENST00000478500.3	n.-85-4231C>T		intron_variant	Intron 2 of 20	1		ENSP00000435778.1

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66881 AN: 151602 Hom.: 14715 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.441 AC: 66918 AN: 151718 Hom.: 14719 Cov.: 32 AF XY: 0.443 AC XY: 32844 AN XY: 74112

African (AFR) AF: 0.399 AC: 16517 AN: 41366

American (AMR) AF: 0.466 AC: 7115 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1902 AN: 3464

East Asian (EAS) AF: 0.485 AC: 2489 AN: 5128

South Asian (SAS) AF: 0.457 AC: 2198 AN: 4812

European-Finnish (FIN) AF: 0.475 AC: 4977 AN: 10468

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30173 AN: 67892

Other (OTH) AF: 0.448 AC: 944 AN: 2108

Alfa AF: 0.443 Hom.: 7895

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.64
PhyloP100		-0.88
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: rs10869335; hg19: chr9-71429146;