NM_003558.4:c.70-6841C>T

Variant names:

• chr9-68856996-C-T
• rs6560397
• NM_003558.4:c.70-6841C>T

Variant summary

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

The NM_003558.4(PIP5K1B):​c.70-6841C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,010 control chromosomes in the GnomAD database, including 13,916 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 0.42 (13916 hom., cov: 32)
• Consequence: PIP5K1B NM_003558.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIP5K1B	NM_003558.4	c.70-6841C>T		intron_variant	Intron 4 of 15	ENST00000265382.8	NP_003549.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIP5K1B	ENST00000265382.8	c.70-6841C>T		intron_variant	Intron 4 of 15	1	NM_003558.4	ENSP00000265382.2
PIP5K1B	ENST00000478500.3	n.190-6841C>T		intron_variant	Intron 5 of 20	1		ENSP00000435778.1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63815 AN: 151892 Hom.: 13913 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.420 AC: 63833 AN: 152010 Hom.: 13916 Cov.: 32 AF XY: 0.419 AC XY: 31164 AN XY: 74298

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.443

Alfa AF: 0.469 Hom.: 34313

Bravo AF: 0.408

Asia WGS AF: 0.307 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.49

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: rs6560397; hg19: chr9-71471912;