rs524
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_014330.5(PPP1R15A):c.1962C>T(p.Ala654=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 1,613,100 control chromosomes in the GnomAD database, including 72,966 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 0.35 ( 10432 hom., cov: 33)
Exomes 𝑓: 0.29 ( 62534 hom. )
Consequence
PPP1R15A
NM_014330.5 synonymous
NM_014330.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.845
Genes affected
PPP1R15A (HGNC:14375): (protein phosphatase 1 regulatory subunit 15A) This gene is a member of a group of genes whose transcript levels are increased following stressful growth arrest conditions and treatment with DNA-damaging agents. The induction of this gene by ionizing radiation occurs in certain cell lines regardless of p53 status, and its protein response is correlated with apoptosis following ionizing radiation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP7
?
Synonymous conserved (PhyloP=0.845 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP1R15A | NM_014330.5 | c.1962C>T | p.Ala654= | synonymous_variant | 3/3 | ENST00000200453.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1R15A | ENST00000200453.6 | c.1962C>T | p.Ala654= | synonymous_variant | 3/3 | 1 | NM_014330.5 | P2 | |
PPP1R15A | ENST00000704027.1 | c.2010C>T | p.Ala670= | synonymous_variant | 2/2 | A2 | |||
PPP1R15A | ENST00000704026.1 | c.1677C>T | p.Ala559= | synonymous_variant | 4/4 | A2 | |||
PPP1R15A | ENST00000600406.2 | c.*817C>T | 3_prime_UTR_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.352 AC: 53441AN: 152032Hom.: 10418 Cov.: 33
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GnomAD3 exomes AF: 0.294 AC: 73739AN: 250696Hom.: 11533 AF XY: 0.294 AC XY: 39794AN XY: 135552
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GnomAD4 exome AF: 0.287 AC: 419609AN: 1460950Hom.: 62534 Cov.: 35 AF XY: 0.288 AC XY: 209280AN XY: 726680
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GnomAD4 genome ? AF: 0.352 AC: 53513AN: 152150Hom.: 10432 Cov.: 33 AF XY: 0.351 AC XY: 26116AN XY: 74380
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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