rs4744712

Variant names:

• chr9-68819791-A-C
• rs4744712
• NM_003558.4:c.-1+1246A>C

Your query was ambiguous. Multiple possible variants found:

• chr9-68819791-A-C
• chr9-68819791-A-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.-1+1246A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,978 control chromosomes in the GnomAD database, including 28,934 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 0.62 (28934 hom., cov: 31)
• Consequence: PIP5K1B NM_003558.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 47 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIP5K1B	NM_003558.4	c.-1+1246A>C		intron_variant	Intron 3 of 15	ENST00000265382.8	NP_003549.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIP5K1B	ENST00000265382.8	c.-1+1246A>C		intron_variant	Intron 3 of 15	1	NM_003558.4	ENSP00000265382.2
PIP5K1B	ENST00000478500.3	n.-1+1246A>C		intron_variant	Intron 3 of 20	1		ENSP00000435778.1

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93427 AN: 151860 Hom.: 28915 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.615 AC: 93491 AN: 151978 Hom.: 28934 Cov.: 31 AF XY: 0.619 AC XY: 45994 AN XY: 74280

African (AFR) AF: 0.583 AC: 24170 AN: 41436

American (AMR) AF: 0.712 AC: 10868 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2222 AN: 3470

East Asian (EAS) AF: 0.547 AC: 2818 AN: 5154

South Asian (SAS) AF: 0.685 AC: 3302 AN: 4820

European-Finnish (FIN) AF: 0.657 AC: 6919 AN: 10536

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41069 AN: 67974

Other (OTH) AF: 0.601 AC: 1268 AN: 2110

Alfa AF: 0.603 Hom.: 48369

Bravo AF: 0.622

Asia WGS AF: 0.632 AC: 2200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.8
DANN	Benign	0.71
PhyloP100		1.3
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: rs4744712; hg19: chr9-71434707; COSMIC: COSV55244226; COSMIC: COSV55244226;