9-68771125-T-C

Variant names:

• chr9-68771125-T-C
• rs7035163
• NM_003558.4:c.-86+28468T>C

Variant summary

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

The NM_003558.4(PIP5K1B):​c.-86+28468T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 151,986 control chromosomes in the GnomAD database, including 33,049 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 0.66 (33049 hom., cov: 30)
• Consequence: PIP5K1B NM_003558.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 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.-86+28468T>C		intron	N/A	NP_003549.1
	PIP5K1B	NM_001376036.1		c.-86+28468T>C		intron	N/A	NP_001362965.1
	PIP5K1B	NM_001376037.1		c.-85-47336T>C		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.-86+28468T>C		intron	N/A	ENSP00000265382.2
	PIP5K1B	ENST00000478500.3	TSL:1	n.-86+28468T>C		intron	N/A	ENSP00000435778.1
	PIP5K1B	ENST00000541509.5	TSL:2	c.-85-47336T>C		intron	N/A	ENSP00000438082.1

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99490 AN: 151866 Hom.: 33019 Cov.: 30

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.655 AC: 99568 AN: 151986 Hom.: 33049 Cov.: 30 AF XY: 0.648 AC XY: 48158 AN XY: 74278

African (AFR) AF: 0.623 AC: 25838 AN: 41442

American (AMR) AF: 0.670 AC: 10233 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2189 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1898 AN: 5174

South Asian (SAS) AF: 0.519 AC: 2495 AN: 4806

European-Finnish (FIN) AF: 0.648 AC: 6838 AN: 10552

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47906 AN: 67952

Other (OTH) AF: 0.664 AC: 1397 AN: 2104

Alfa AF: 0.688 Hom.: 139494

Bravo AF: 0.653

Asia WGS AF: 0.454 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.33
PhyloP100		-0.16
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: rs7035163; hg19: chr9-71386041;