chr6-150184569-T-G

Variant names:

• chr6-150184569-T-G
• rs2144400
• NM_030949.3:c.307-30175T>G

Variant summary

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

The NM_030949.3(PPP1R14C):​c.307-30175T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 151,630 control chromosomes in the GnomAD database, including 59,417 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 0.88 (59417 hom., cov: 28)
• Consequence: PPP1R14C NM_030949.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R14C	NM_030949.3	c.307-30175T>G		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.307-30175T>G		intron_variant	Intron 1 of 3	1	NM_030949.3	ENSP00000355260.4

Frequencies

GnomAD3 genomes AF: 0.882 AC: 133700 AN: 151512 Hom.: 59355 Cov.: 28

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.883 AC: 133821 AN: 151630 Hom.: 59417 Cov.: 28 AF XY: 0.887 AC XY: 65720 AN XY: 74052

Gnomad4 AFR AF: 0.964

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.954

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.868

Alfa AF: 0.865 Hom.: 10241

Bravo AF: 0.887

Asia WGS AF: 0.971 AC: 3378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.090
DANN	Benign	0.55

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: rs2144400; hg19: chr6-150505705; COSMIC: COSV63173453;