chr2-68188635-G-A
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_000945.4(PPP3R1):c.99C>T(p.Asp33=) variant causes a synonymous change. The variant allele was found at a frequency of 0.429 in 1,611,810 control chromosomes in the GnomAD database, including 152,011 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.46 ( 16010 hom., cov: 31)
Exomes 𝑓: 0.43 ( 136001 hom. )
Consequence
PPP3R1
NM_000945.4 synonymous
NM_000945.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 5.12
Genes affected
PPP3R1 (HGNC:9317): (protein phosphatase 3 regulatory subunit B, alpha) Enables cyclosporin A binding activity; phosphatase binding activity; and protein domain specific binding activity. Involved in calcineurin-NFAT signaling cascade and positive regulation of transcription by RNA polymerase II. Part of calcineurin complex. Implicated in Alzheimer's disease and dilated cardiomyopathy. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 2-68188635-G-A is Benign according to our data. Variant chr2-68188635-G-A is described in ClinVar as [Benign]. Clinvar id is 1181494.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP3R1 | NM_000945.4 | c.99C>T | p.Asp33= | synonymous_variant | 3/6 | ENST00000234310.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP3R1 | ENST00000234310.8 | c.99C>T | p.Asp33= | synonymous_variant | 3/6 | 1 | NM_000945.4 | P1 | |
PPP3R1 | ENST00000409752.5 | c.156C>T | p.Asp52= | synonymous_variant | 3/6 | 3 | |||
PPP3R1 | ENST00000409377.1 | c.69C>T | p.Asp23= | synonymous_variant | 3/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.455 AC: 69109AN: 151774Hom.: 15994 Cov.: 31
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GnomAD3 exomes AF: 0.473 AC: 117015AN: 247438Hom.: 28599 AF XY: 0.480 AC XY: 64440AN XY: 134372
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GnomAD4 exome AF: 0.426 AC: 621984AN: 1459918Hom.: 136001 Cov.: 37 AF XY: 0.432 AC XY: 314112AN XY: 726282
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GnomAD4 genome AF: 0.455 AC: 69174AN: 151892Hom.: 16010 Cov.: 31 AF XY: 0.464 AC XY: 34425AN XY: 74238
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 15, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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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