chr6-150150127-C-T

Variant names:

• chr6-150150127-C-T
• rs1408505
• NM_030949.3:c.306+6629C>T

Variant summary

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

The NM_030949.3(PPP1R14C):​c.306+6629C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,166 control chromosomes in the GnomAD database, including 3,729 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 0.22 (3729 hom., cov: 32)
• Consequence: PPP1R14C NM_030949.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 7 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R14C	NM_030949.3	c.306+6629C>T		intron_variant	Intron 1 of 3	ENST00000361131.5	NP_112211.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R14C	ENST00000361131.5	c.306+6629C>T		intron_variant	Intron 1 of 3	1	NM_030949.3	ENSP00000355260.4

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32697 AN: 152048 Hom.: 3728 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.215 AC: 32731 AN: 152166 Hom.: 3729 Cov.: 32 AF XY: 0.219 AC XY: 16271 AN XY: 74392

African (AFR) AF: 0.184 AC: 7654 AN: 41516

American (AMR) AF: 0.273 AC: 4175 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3466

East Asian (EAS) AF: 0.0303 AC: 157 AN: 5186

South Asian (SAS) AF: 0.305 AC: 1472 AN: 4820

European-Finnish (FIN) AF: 0.273 AC: 2880 AN: 10564

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15190 AN: 68002

Other (OTH) AF: 0.192 AC: 406 AN: 2110

Alfa AF: 0.218 Hom.: 5076

Bravo AF: 0.215

Asia WGS AF: 0.184 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.2
DANN	Benign	0.70
PhyloP100		0.33
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: rs1408505; hg19: chr6-150471263;