rs587778622
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_014225.6(PPP2R1A):āc.75T>Gā(p.Val25=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000202 in 1,550,678 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.00022 ( 0 hom., cov: 33)
Exomes š: 0.00020 ( 3 hom. )
Consequence
PPP2R1A
NM_014225.6 synonymous
NM_014225.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.170
Genes affected
PPP2R1A (HGNC:9302): (protein phosphatase 2 scaffold subunit Aalpha) This gene encodes a constant regulatory subunit of protein phosphatase 2. Protein phosphatase 2 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 constant regulatory subunit A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit. This gene encodes an alpha isoform of the constant regulatory subunit A. Alternatively spliced transcript variants have been described. [provided by RefSeq, Apr 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
Variant 19-52190171-T-G is Benign according to our data. Variant chr19-52190171-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 135073.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.17 with no splicing effect.
BS2
?
High AC in GnomAd4 at 33 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R1A | NM_014225.6 | c.75T>G | p.Val25= | synonymous_variant | 1/15 | ENST00000322088.11 | |
PPP2R1A | NR_033500.2 | n.120T>G | non_coding_transcript_exon_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R1A | ENST00000322088.11 | c.75T>G | p.Val25= | synonymous_variant | 1/15 | 1 | NM_014225.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152146Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000540 AC: 83AN: 153564Hom.: 0 AF XY: 0.000505 AC XY: 41AN XY: 81180
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GnomAD4 exome AF: 0.000201 AC: 281AN: 1398532Hom.: 3 Cov.: 32 AF XY: 0.000204 AC XY: 141AN XY: 689824
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GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152146Hom.: 0 Cov.: 33 AF XY: 0.000229 AC XY: 17AN XY: 74322
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 14, 2023 | - - |
Houge-Janssens syndrome 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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