rs17682482

Positions:

• chr12-110716983-C-G

Variant summary

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

The XM_011538504.4(PPP1CC):​c.944-1836G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0828 in 152,270 control chromosomes in the GnomAD database, including 572 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 0.083 (572 hom., cov: 32)
• Consequence: PPP1CC XM_011538504.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593

Genes affected

PPP1CC (HGNC:9283): (protein phosphatase 1 catalytic subunit gamma) The protein encoded by this gene belongs to the protein phosphatase family, PP1 subfamily. PP1 is an ubiquitous serine/threonine phosphatase that regulates many cellular processes, including cell division. It is expressed in mammalian cells as three closely related isoforms, alpha, beta/delta and gamma, which have distinct localization patterns. This gene encodes the gamma isozyme. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP1CC	XM_011538504.4	c.944-1836G>C		intron_variant			XP_011536806.1
PPP1CC	XM_011538505.4	c.943+4122G>C		intron_variant			XP_011536807.1
		n.110716983C>G		intergenic_region
PPP1CC	XR_007063094.1	n.1128-1836G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0829 AC: 12611 AN: 152152 Hom.: 574 Cov.: 32

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.00519

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0890

Gnomad OTH AF: 0.0899

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

GnomAD4 genome AF: 0.0828 AC: 12604 AN: 152270 Hom.: 572 Cov.: 32 AF XY: 0.0810 AC XY: 6034 AN XY: 74460

Gnomad4 AFR AF: 0.0917

Gnomad4 AMR AF: 0.0550

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.00520

Gnomad4 SAS AF: 0.0976

Gnomad4 FIN AF: 0.0569

Gnomad4 NFE AF: 0.0890

Gnomad4 OTH AF: 0.0889

Alfa AF: 0.0852 Hom.: 71

Bravo AF: 0.0813

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17682482; hg19: chr12-111154788;