chr14-101818979-T-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001352913.2(PPP2R5C):c.259+32796T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000177 in 1,525,720 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
PPP2R5C
NM_001352913.2 intron
NM_001352913.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.140
Genes affected
PPP2R5C (HGNC:9311): (protein phosphatase 2 regulatory subunit B'gamma) The product of this gene belongs to the phosphatase 2A regulatory subunit B family. Protein phosphatase 2A is one of the four major Ser/Thr phosphatases, and it is implicated in the negative control of cell growth and division. It consists of a common heteromeric core enzyme, which is composed of a catalytic subunit and a constant regulatory subunit, that associates with a variety of regulatory subunits. The B regulatory subunit might modulate substrate selectivity and catalytic activity. This gene encodes a gamma isoform of the regulatory subunit B56 subfamily. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 14-101818979-T-G is Benign according to our data. Variant chr14-101818979-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 1656183.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R5C | NM_001352913.2 | c.259+32796T>G | intron_variant | ENST00000694906.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R5C | ENST00000694906.1 | c.259+32796T>G | intron_variant | NM_001352913.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152200Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000260 AC: 4AN: 153862Hom.: 0 AF XY: 0.0000367 AC XY: 3AN XY: 81638
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GnomAD4 exome AF: 0.0000131 AC: 18AN: 1373520Hom.: 0 Cov.: 28 AF XY: 0.0000118 AC XY: 8AN XY: 678910
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GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74342
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 25, 2021 | - - |
Computational 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