rs11558236

Variant names:

• chr12-110720423-A-C
• rs11558236
• NM_002710.4:c.*653T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-110720423-A-C
• chr12-110720423-A-G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_002710.4(PPP1CC):​c.*653T>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.00000308 in 324,450 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000031 (0 hom.)
• Consequence: PPP1CC NM_002710.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.61
• 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=-0.27).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1CC	NM_002710.4	c.*653T>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000335007.10	NP_002701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1CC	ENST00000335007.10	c.*653T>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_002710.4	ENSP00000335084.5
PPP1CC	ENST00000550261.5	n.*363-219T>G		intron_variant	Intron 4 of 4	5		ENSP00000447528.2
PPP1CC	ENST00000546904.1	n.1076T>G		non_coding_transcript_exon_variant	Exon 2 of 2	2
PPP1CC	ENST00000340766.9	c.944-219T>G		intron_variant	Intron 7 of 7	2		ENSP00000341779.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000308 AC: 1 AN: 324450 Hom.: 0 Cov.: 0 AF XY: 0.00000586 AC XY: 1 AN XY: 170678

African (AFR) AF: 0.00 AC: 0 AN: 8760

American (AMR) AF: 0.00 AC: 0 AN: 11330

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10740

East Asian (EAS) AF: 0.0000410 AC: 1 AN: 24366

South Asian (SAS) AF: 0.00 AC: 0 AN: 24560

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 22262

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1504

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 201198

Other (OTH) AF: 0.00 AC: 0 AN: 19730

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	14
DANN	Benign	0.90
PhyloP100		6.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs11558236; hg19: chr12-111158228;