rs2503706
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002744.6(PRKCZ):c.421-398A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 161,426 control chromosomes in the GnomAD database, including 48,488 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 0.77 ( 46088 hom., cov: 33)
Exomes 𝑓: 0.71 ( 2400 hom. )
Consequence
PRKCZ
NM_002744.6 intron
NM_002744.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.02
Genes affected
PRKCZ (HGNC:9412): (protein kinase C zeta) Protein kinase C (PKC) zeta is a member of the PKC family of serine/threonine kinases which are involved in a variety of cellular processes such as proliferation, differentiation and secretion. Unlike the classical PKC isoenzymes which are calcium-dependent, PKC zeta exhibits a kinase activity which is independent of calcium and diacylglycerol but not of phosphatidylserine. Furthermore, it is insensitive to typical PKC inhibitors and cannot be activated by phorbol ester. Unlike the classical PKC isoenzymes, it has only a single zinc finger module. These structural and biochemical properties indicate that the zeta subspecies is related to, but distinct from other isoenzymes of PKC. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
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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=-0.96).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKCZ | NM_002744.6 | c.421-398A>G | intron_variant | ENST00000378567.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKCZ | ENST00000378567.8 | c.421-398A>G | intron_variant | 1 | NM_002744.6 | P1 | |||
ENST00000606533.1 | n.1468T>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.769 AC: 116922AN: 152096Hom.: 46016 Cov.: 33
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GnomAD4 exome AF: 0.714 AC: 6581AN: 9212Hom.: 2400 Cov.: 0 AF XY: 0.707 AC XY: 3328AN XY: 4706
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GnomAD4 genome ? AF: 0.769 AC: 117055AN: 152214Hom.: 46088 Cov.: 33 AF XY: 0.771 AC XY: 57385AN XY: 74414
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ClinVar
Not reported inComputational scores
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Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at