rs663532
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_006257.5(PRKCQ):c.*413A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0173 in 194,276 control chromosomes in the GnomAD database, including 48 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 0.019 ( 45 hom., cov: 33)
Exomes 𝑓: 0.012 ( 3 hom. )
Consequence
PRKCQ
NM_006257.5 3_prime_UTR
NM_006257.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.811
Genes affected
PRKCQ (HGNC:9410): (protein kinase C theta) Protein kinase C (PKC) is a family of serine- and threonine-specific protein kinases that can be activated by calcium and the second messenger diacylglycerol. PKC family members phosphorylate a wide variety of protein targets and are known to be involved in diverse cellular signaling pathways. PKC family members also serve as major receptors for phorbol esters, a class of tumor promoters. Each member of the PKC family has a specific expression profile and is believed to play a distinct role. The protein encoded by this gene is one of the PKC family members. It is a calcium-independent and phospholipid-dependent protein kinase. This kinase is important for T-cell activation. It is required for the activation of the transcription factors NF-kappaB and AP-1, and may link the T cell receptor (TCR) signaling complex to the activation of the transcription factors. [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=-0.89).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0188 (2859/152294) while in subpopulation AFR AF= 0.0306 (1271/41554). AF 95% confidence interval is 0.0292. There are 45 homozygotes in gnomad4. There are 1432 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2854 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKCQ | NM_006257.5 | c.*413A>G | 3_prime_UTR_variant | 18/18 | ENST00000263125.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKCQ | ENST00000263125.10 | c.*413A>G | 3_prime_UTR_variant | 18/18 | 1 | NM_006257.5 | P1 | ||
PRKCQ | ENST00000397176.6 | c.*413A>G | 3_prime_UTR_variant | 17/17 | 5 | ||||
PRKCQ | ENST00000539722.5 | c.*413A>G | 3_prime_UTR_variant | 17/17 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0188 AC: 2854AN: 152176Hom.: 44 Cov.: 33
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GnomAD4 exome AF: 0.0119 AC: 498AN: 41982Hom.: 3 Cov.: 0 AF XY: 0.0118 AC XY: 259AN XY: 21892
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GnomAD4 genome ? AF: 0.0188 AC: 2859AN: 152294Hom.: 45 Cov.: 33 AF XY: 0.0192 AC XY: 1432AN XY: 74458
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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