rs7960761
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002710.4(PPP1CC):c.419-1846A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,076 control chromosomes in the GnomAD database, including 1,186 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 0.12 ( 1186 hom., cov: 32)
Exomes 𝑓: 0.12 ( 0 hom. )
Consequence
PPP1CC
NM_002710.4 intron
NM_002710.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.444
Genes affected
PPP1CC (HGNC:9283): (protein phosphatase 1 catalytic subunit gamma) The protein encoded by this gene belongs to the protein phosphatase family, PP1 subfamily. PP1 is an ubiquitous serine/threonine phosphatase that regulates many cellular processes, including cell division. It is expressed in mammalian cells as three closely related isoforms, alpha, beta/delta and gamma, which have distinct localization patterns. This gene encodes the gamma isozyme. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 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=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP1CC | NM_002710.4 | c.419-1846A>G | intron_variant | ENST00000335007.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1CC | ENST00000335007.10 | c.419-1846A>G | intron_variant | 1 | NM_002710.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.116 AC: 17583AN: 151924Hom.: 1185 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.118 AC: 4AN: 34Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 4AN XY: 24
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GnomAD4 genome ? AF: 0.116 AC: 17601AN: 152042Hom.: 1186 Cov.: 32 AF XY: 0.113 AC XY: 8378AN XY: 74334
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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