rs524

Variant names:

• chr19-48875910-C-A
• rs524
• NM_014330.5:c.1962C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-48875910-C-A
• chr19-48875910-C-G
• chr19-48875910-C-T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_014330.5(PPP1R15A):​c.1962C>A​(p.Ala654Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: PPP1R15A NM_014330.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.845
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BP7: Synonymous conserved (PhyloP=0.845 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014330.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R15A	NM_014330.5	MANE Select	c.1962C>A	p.Ala654Ala	synonymous	Exon 3 of 3	NP_055145.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R15A	ENST00000200453.6	TSL:1 MANE Select	c.1962C>A	p.Ala654Ala	synonymous	Exon 3 of 3	ENSP00000200453.4
	PPP1R15A	ENST00000704027.1		c.2010C>A	p.Ala670Ala	synonymous	Exon 2 of 2	ENSP00000515637.1
	PPP1R15A	ENST00000704026.1		c.1677C>A	p.Ala559Ala	synonymous	Exon 4 of 4	ENSP00000515636.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.1
DANN	Benign	0.71
PhyloP100		0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs524; hg19: chr19-49379167;