Genetic Variant PPP1R14C:c.*911A>G (chr6-150249731-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_030949.3(PPP1R14C):c.*911A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0547 in 396,106 control chromosomes in the GnomAD database, including 701 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 0.057 ( 288 hom., cov: 32)

Exomes 𝑓: 0.053 ( 413 hom. )

Consequence

PPP1R14C
NM_030949.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.40

Variant links:

Genes affected

PPP1R14C (HGNC:14952): (protein phosphatase 1 regulatory inhibitor subunit 14C) The degree of protein phosphorylation is regulated by a balance of protein kinase and phosphatase activities. Protein phosphatase-1 (PP1; see MIM 176875) is a signal-transducing phosphatase that influences neuronal activity, protein synthesis, metabolism, muscle contraction, and cell division. PPP1R14C is an inhibitor of PP1 (Liu et al., 2002 [PubMed 11812771]).[supplied by OMIM, Feb 2010]

PPP1R14C links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R14C	NM_030949.3 link	c.*911A>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000361131.5	NP_112211.1	Q8TAE6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R14C	ENST00000361131.5 link	c.*911A>G		3_prime_UTR_variant	Exon 4 of 4	1	NM_030949.3	ENSP00000355260.4		Q8TAE6

Frequencies

GnomAD3 genomes

AF:

0.0574

AC:

8735

AN:

152140

Hom.:

285

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0763

Gnomad AMI

AF:

0.0735

Gnomad AMR

AF:

0.0505

Gnomad ASJ

AF:

0.0706

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.0685

Gnomad FIN

AF:

0.0604

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0413

Gnomad OTH

AF:

0.0741

GnomAD4 exome

AF:

0.0529

AC:

12908

AN:

243848

Hom.:

413

Cov.:

AF XY:

0.0530

AC XY:

6552

AN XY:

123564

show subpopulations

Gnomad4 AFR exome

AF:

0.0813

Gnomad4 AMR exome

AF:

0.0438

Gnomad4 ASJ exome

AF:

0.0830

Gnomad4 EAS exome

AF:

0.0965

Gnomad4 SAS exome

AF:

0.0636

Gnomad4 FIN exome

AF:

0.0572

Gnomad4 NFE exome

AF:

0.0416

Gnomad4 OTH exome

AF:

0.0657

GnomAD4 genome

AF:

0.0575

AC:

8748

AN:

152258

Hom.:

288

Cov.:

AF XY:

0.0589

AC XY:

4388

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.0765

Gnomad4 AMR

AF:

0.0504

Gnomad4 ASJ

AF:

0.0706

Gnomad4 EAS

AF:

0.102

Gnomad4 SAS

AF:

0.0678

Gnomad4 FIN

AF:

0.0604

Gnomad4 NFE

AF:

0.0413

Gnomad4 OTH

AF:

0.0743

Alfa

AF:

0.0446

Hom.:

310

Bravo

AF:

0.0579

Asia WGS

AF:

0.123

AC:

431

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

7.5

DANN

Benign

0.66

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over