rs963707

Positions:

• chr9-68740301-C-T

Variant summary

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

The ENST00000265382.8(PIP5K1B):​c.-242-2200C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,198 control chromosomes in the GnomAD database, including 41,967 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 0.73 (41967 hom., cov: 32)
• Consequence: PIP5K1B ENST00000265382.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356

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 (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIP5K1B	NM_003558.4	c.-242-2200C>T		intron_variant		ENST00000265382.8	NP_003549.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIP5K1B	ENST00000265382.8	c.-242-2200C>T		intron_variant		1	NM_003558.4	ENSP00000265382	P1
PIP5K1B	ENST00000377284.5	c.-243+409C>T		intron_variant		3		ENSP00000366498
PIP5K1B	ENST00000541509.5	c.-86+34539C>T		intron_variant		2		ENSP00000438082
PIP5K1B	ENST00000472907.6	n.497-2200C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111470 AN: 152080 Hom.: 41918 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.733 AC: 111577 AN: 152198 Hom.: 41967 Cov.: 32 AF XY: 0.730 AC XY: 54321 AN XY: 74396

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.722

Alfa AF: 0.672 Hom.: 13711

Bravo AF: 0.740

Asia WGS AF: 0.766 AC: 2664 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	3.4
DANN	Benign	0.39

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: rs963707; hg19: chr9-71355217;