rs3215826
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_005028.5(PIP4K2A):c.*842del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.66 ( 32910 hom., cov: 0)
Exomes 𝑓: 0.64 ( 44062 hom. )
Consequence
PIP4K2A
NM_005028.5 3_prime_UTR
NM_005028.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.394
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 -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIP4K2A | NM_005028.5 | c.*842del | 3_prime_UTR_variant | 10/10 | ENST00000376573.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIP4K2A | ENST00000376573.9 | c.*842del | 3_prime_UTR_variant | 10/10 | 1 | NM_005028.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.657 AC: 99725AN: 151676Hom.: 32883 Cov.: 0
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GnomAD4 exome AF: 0.640 AC: 136552AN: 213238Hom.: 44062 Cov.: 0 AF XY: 0.640 AC XY: 68686AN XY: 107290
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GnomAD4 genome ? AF: 0.658 AC: 99807AN: 151796Hom.: 32910 Cov.: 0 AF XY: 0.665 AC XY: 49311AN XY: 74148
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ClinVar
Not reported inComputational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at