rs2035980

chr7-114068445-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000449795.5(PPP1R3A):c.-182+7181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,952 control chromosomes in the GnomAD database, including 28,526 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 0.61 (28526 hom., cov: 32)
• Consequence: PPP1R3A ENST00000449795.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

Genes affected

PPP1R3A (HGNC:9291): (protein phosphatase 1 regulatory subunit 3A) The glycogen-associated form of protein phosphatase-1 (PP1) derived from skeletal muscle is a heterodimer composed of a 37-kD catalytic subunit and a 124-kD targeting and regulatory subunit. This gene encodes the regulatory subunit which binds to muscle glycogen with high affinity, thereby enhancing dephosphorylation of glycogen-bound substrates for PP1 such as glycogen synthase and glycogen phosphorylase kinase. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R3A	ENST00000449795.5	c.-182+7181C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92632 AN: 151832 Hom.: 28512 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.625

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.610 AC: 92698 AN: 151952 Hom.: 28526 Cov.: 32 AF XY: 0.618 AC XY: 45908 AN XY: 74284

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.626

Alfa AF: 0.625 Hom.: 7703

Bravo AF: 0.591

Asia WGS AF: 0.627 AC: 2181 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.93
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2035980; hg19: chr7-113708500;