chr6-150243430-G-A

Variant names:

• chr6-150243430-G-A
• rs1086204
• NM_030949.3:c.424-5316G>A

Variant summary

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

The NM_030949.3(PPP1R14C):​c.424-5316G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0476 in 152,038 control chromosomes in the GnomAD database, including 255 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 0.048 (255 hom., cov: 32)
• Consequence: PPP1R14C NM_030949.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 2 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0673 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.424-5316G>A		intron	N/A	NP_112211.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R14C	ENST00000361131.5	TSL:1 MANE Select	c.424-5316G>A		intron	N/A	ENSP00000355260.4

Frequencies

GnomAD3 genomes AF: 0.0476 AC: 7239 AN: 151922 Hom.: 255 Cov.: 32

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0260

Gnomad FIN AF: 0.0757

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.0514

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

GnomAD4 genome AF: 0.0476 AC: 7237 AN: 152038 Hom.: 255 Cov.: 32 AF XY: 0.0468 AC XY: 3480 AN XY: 74328

African (AFR) AF: 0.0108 AC: 448 AN: 41464

American (AMR) AF: 0.0395 AC: 603 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0262 AC: 126 AN: 4810

European-Finnish (FIN) AF: 0.0757 AC: 798 AN: 10544

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0690 AC: 4689 AN: 67980

Other (OTH) AF: 0.0509 AC: 107 AN: 2104

Alfa AF: 0.0588 Hom.: 41

Bravo AF: 0.0440

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.68
PhyloP100		-1.5
Mutation Taster		=100/0	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: rs1086204; hg19: chr6-150564566;