rs2272080
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005605.5(PPP3CC):c.-197T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 462,214 control chromosomes in the GnomAD database, including 5,995 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 0.17 ( 4433 hom., cov: 33)
Exomes 𝑓: 0.075 ( 1562 hom. )
Consequence
PPP3CC
NM_005605.5 5_prime_UTR
NM_005605.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0830
Genes affected
PPP3CC (HGNC:9316): (protein phosphatase 3 catalytic subunit gamma) Calcineurin is a calcium-dependent, calmodulin-stimulated protein phosphatase involved in the downstream regulation of dopaminergic signal transduction. Calcineurin is composed of a regulatory subunit and a catalytic subunit. The protein encoded by this gene represents one of the regulatory subunits that has been found for calcineurin. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
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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=-0.74).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP3CC | NM_005605.5 | c.-197T>G | 5_prime_UTR_variant | 1/14 | ENST00000240139.10 | NP_005596.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP3CC | ENST00000240139.10 | c.-197T>G | 5_prime_UTR_variant | 1/14 | 1 | NM_005605.5 | ENSP00000240139 | P3 | ||
PPP3CC | ENST00000289963.12 | c.-197T>G | 5_prime_UTR_variant | 1/13 | 1 | ENSP00000289963 | A1 | |||
PPP3CC | ENST00000397775.7 | c.-197T>G | 5_prime_UTR_variant | 1/15 | 2 | ENSP00000380878 | ||||
PPP3CC | ENST00000518852.5 | c.-197T>G | 5_prime_UTR_variant | 1/8 | 2 | ENSP00000429379 |
Frequencies
GnomAD3 genomes AF: 0.174 AC: 26480AN: 151948Hom.: 4408 Cov.: 33
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GnomAD4 exome AF: 0.0751 AC: 23296AN: 310158Hom.: 1562 Cov.: 4 AF XY: 0.0740 AC XY: 12000AN XY: 162068
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GnomAD4 genome AF: 0.175 AC: 26565AN: 152056Hom.: 4433 Cov.: 33 AF XY: 0.170 AC XY: 12673AN XY: 74350
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at