rs4744712

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.28
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
PIP5K1BNM_003558.4 linkuse as main transcriptc.-1+1246A>C intron_variant ENST00000265382.8 NP_003549.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PIP5K1BENST00000265382.8 linkuse as main transcriptc.-1+1246A>C intron_variant 1 NM_003558.4 ENSP00000265382 P1O14986-1

Frequencies

GnomAD3 genomes
AF:
0.615
AC:
93427
AN:
151860
Hom.:
28915
Cov.:
31
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.583
Gnomad4 AMR
AF:
0.712
Gnomad4 ASJ
AF:
0.640
Gnomad4 EAS
AF:
0.547
Gnomad4 SAS
AF:
0.685
Gnomad4 FIN
AF:
0.657
Gnomad4 NFE
AF:
0.604
Gnomad4 OTH
AF:
0.601
Alfa
AF:
0.562
Hom.:
5046
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

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4744712; hg19: chr9-71434707; COSMIC: COSV55244226; COSMIC: COSV55244226; API