2-182020469-C-T

Position:

• chr2-182020469-C-T

Variant summary

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

The NM_001080545.3(PPP1R1C):​c.142+32570C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.928 in 152,242 control chromosomes in the GnomAD database, including 65,680 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 0.93 (65680 hom., cov: 31)
• Consequence: PPP1R1C NM_001080545.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

PPP1R1C (HGNC:14940): (protein phosphatase 1 regulatory inhibitor subunit 1C) Protein phosphatase-1 (PP1) is a major serine/threonine phosphatase that regulates a variety of cellular functions. PP1 consists of a catalytic subunit (see PPP1CA; MIM 176875) and regulatory subunits that determine the subcellular localization of PP1 or regulate its function. PPP1R1C belongs to a group of PP1 inhibitory subunits that are themselves regulated by phosphorylation (Wang et al., 2008 [PubMed 18310074]).[supplied by OMIM, Feb 2010]

PPP1R1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP1R1C	NM_001080545.3	c.142+32570C>T		intron_variant		ENST00000682840.1	NP_001074014.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R1C	ENST00000682840.1	c.142+32570C>T		intron_variant			NM_001080545.3	ENSP00000507052.1

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141100 AN: 152124 Hom.: 65628 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.928 AC: 141214 AN: 152242 Hom.: 65680 Cov.: 31 AF XY: 0.929 AC XY: 69143 AN XY: 74434

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.937

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.968

Gnomad4 OTH AF: 0.936

Alfa AF: 0.956 Hom.: 63961

Bravo AF: 0.918

Asia WGS AF: 0.913 AC: 3176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.33
DANN	Benign	0.60

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

Publications

LitVar

Other links and lift over

dbSNP: rs1196184; hg19: chr2-182885196;