chr12-110742702-C-A

Variant names:

• chr12-110742702-C-A
• rs367543177
• NM_002710.4:c.6G>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4 BP7

The NM_002710.4(PPP1CC):​c.6G>T​(p.Ala2Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PPP1CC NM_002710.4 synonymous
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 3.01
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.11).
• BP7: Synonymous conserved (PhyloP=3.01 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002710.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1CC	NM_002710.4	MANE Select	c.6G>T	p.Ala2Ala	synonymous	Exon 1 of 7	NP_002701.1	P36873-1
	PPP1CC	NM_001244974.2		c.6G>T	p.Ala2Ala	synonymous	Exon 1 of 8	NP_001231903.1	P36873-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1CC	ENST00000335007.10	TSL:1 MANE Select	c.6G>T	p.Ala2Ala	synonymous	Exon 1 of 7	ENSP00000335084.5	P36873-1
	PPP1CC	ENST00000340766.9	TSL:2	c.6G>T	p.Ala2Ala	synonymous	Exon 1 of 8	ENSP00000341779.5	P36873-2
	PPP1CC	ENST00000550991.5	TSL:2	c.6G>T	p.Ala2Ala	synonymous	Exon 1 of 6	ENSP00000448981.1	F8VYE8

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1303708 Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0 AN XY: 644024

African (AFR) AF: 0.00 AC: 0 AN: 27694

American (AMR) AF: 0.00 AC: 0 AN: 30306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21870

East Asian (EAS) AF: 0.00 AC: 0 AN: 31082

South Asian (SAS) AF: 0.00 AC: 0 AN: 63348

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46940

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5210

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1025094

Other (OTH) AF: 0.00 AC: 0 AN: 52164

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: not provided

Revision: no classification provided

Pathogenic	VUS	Benign	Condition
-	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.11
CADD	Benign	16
DANN	Benign	0.96
PhyloP100		3.0
PromoterAI		-0.17	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs367543177; hg19: chr12-111180507;