rs10508649
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_005028.5(PIP4K2A):āc.597A>Gā(p.Val199=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0201 in 1,613,658 control chromosomes in the GnomAD database, including 1,809 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: š 0.066 ( 884 hom., cov: 33)
Exomes š: 0.015 ( 925 hom. )
Consequence
PIP4K2A
NM_005028.5 synonymous
NM_005028.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.282
Genes affected
PIP4K2A (HGNC:8997): (phosphatidylinositol-5-phosphate 4-kinase type 2 alpha) Phosphatidylinositol-5,4-bisphosphate, the precursor to second messengers of the phosphoinositide signal transduction pathways, is thought to be involved in the regulation of secretion, cell proliferation, differentiation, and motility. The protein encoded by this gene is one of a family of enzymes capable of catalyzing the phosphorylation of phosphatidylinositol-5-phosphate on the fourth hydroxyl of the myo-inositol ring to form phosphatidylinositol-5,4-bisphosphate. The amino acid sequence of this enzyme does not show homology to other kinases, but the recombinant protein does exhibit kinase activity. This gene is a member of the phosphatidylinositol-5-phosphate 4-kinase family. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP7
?
Synonymous conserved (PhyloP=-0.282 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIP4K2A | NM_005028.5 | c.597A>G | p.Val199= | synonymous_variant | 5/10 | ENST00000376573.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIP4K2A | ENST00000376573.9 | c.597A>G | p.Val199= | synonymous_variant | 5/10 | 1 | NM_005028.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0661 AC: 10059AN: 152212Hom.: 881 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0266 AC: 6670AN: 250964Hom.: 420 AF XY: 0.0220 AC XY: 2988AN XY: 135640
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GnomAD4 exome AF: 0.0153 AC: 22395AN: 1461328Hom.: 925 Cov.: 30 AF XY: 0.0144 AC XY: 10434AN XY: 727000
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GnomAD4 genome ? AF: 0.0662 AC: 10087AN: 152330Hom.: 884 Cov.: 33 AF XY: 0.0641 AC XY: 4775AN XY: 74498
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at