NM_030949.3:c.*911A>G

Variant names:

• chr6-150249731-A-G
• rs3734729
• NM_030949.3:c.*911A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 9 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030949.3. 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
	PPP1R14C	NM_030949.3	MANE Select	c.*911A>G		3_prime_UTR	Exon 4 of 4	NP_112211.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R14C	ENST00000361131.5	TSL:1 MANE Select	c.*911A>G		3_prime_UTR	Exon 4 of 4	ENSP00000355260.4

Frequencies

GnomAD3 genomes AF: 0.0574 AC: 8735 AN: 152140 Hom.: 285 Cov.: 32

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.: 0 AF XY: 0.0530 AC XY: 6552 AN XY: 123564

African (AFR) AF: 0.0813 AC: 581 AN: 7150

American (AMR) AF: 0.0438 AC: 323 AN: 7378

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 763 AN: 9198

East Asian (EAS) AF: 0.0965 AC: 2199 AN: 22792

South Asian (SAS) AF: 0.0636 AC: 139 AN: 2184

European-Finnish (FIN) AF: 0.0572 AC: 1181 AN: 20640

Middle Eastern (MID) AF: 0.0914 AC: 117 AN: 1280

European-Non Finnish (NFE) AF: 0.0416 AC: 6536 AN: 156966

Other (OTH) AF: 0.0657 AC: 1069 AN: 16260

GnomAD4 genome AF: 0.0575 AC: 8748 AN: 152258 Hom.: 288 Cov.: 32 AF XY: 0.0589 AC XY: 4388 AN XY: 74468

African (AFR) AF: 0.0765 AC: 3175 AN: 41522

American (AMR) AF: 0.0504 AC: 771 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0706 AC: 245 AN: 3470

East Asian (EAS) AF: 0.102 AC: 529 AN: 5188

South Asian (SAS) AF: 0.0678 AC: 327 AN: 4826

European-Finnish (FIN) AF: 0.0604 AC: 641 AN: 10614

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0413 AC: 2812 AN: 68020

Other (OTH) AF: 0.0743 AC: 157 AN: 2114

Alfa AF: 0.0463 Hom.: 739

Bravo AF: 0.0579

Asia WGS AF: 0.123 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.5
DANN	Benign	0.66
PhyloP100		1.4
Mutation Taster		=99/1	polymorphism (auto)

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: rs3734729; hg19: chr6-150570867;