2-28802613-A-G

Position:

• chr2-28802613-A-G

Variant summary

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

The NM_002709.3(PPP1CB):​c.*3310A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 152,096 control chromosomes in the GnomAD database, including 20,288 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 0.51 (20288 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PPP1CB NM_002709.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

Genes affected

PPP1CB (HGNC:9282): (protein phosphatase 1 catalytic subunit beta) The protein encoded by this gene is one of the three catalytic subunits of protein phosphatase 1 (PP1). PP1 is a serine/threonine specific protein phosphatase known to be involved in the regulation of a variety of cellular processes, such as cell division, glycogen metabolism, muscle contractility, protein synthesis, and HIV-1 viral transcription. Mouse studies suggest that PP1 functions as a suppressor of learning and memory. Two alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]

SPDYA (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP1CB	NM_002709.3	c.*3310A>G		3_prime_UTR_variant	8/8	ENST00000395366.3	NP_002700.1
PPP1CB	NM_206876.2	c.*3310A>G		3_prime_UTR_variant	9/9		NP_996759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1CB	ENST00000395366.3	c.*3310A>G		3_prime_UTR_variant	8/8	1	NM_002709.3	ENSP00000378769.2
PPP1CB	ENST00000455580.6	c.*3310A>G		3_prime_UTR_variant	8/8	3		ENSP00000390715.2
SPDYA	ENST00000462832.5	n.807+3314A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77182 AN: 151978 Hom.: 20277 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.533

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.508 AC: 77220 AN: 152096 Hom.: 20288 Cov.: 32 AF XY: 0.508 AC XY: 37800 AN XY: 74364

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.535

Alfa AF: 0.564 Hom.: 29574

Bravo AF: 0.489

Asia WGS AF: 0.408 AC: 1422 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	0.021
DANN	Benign	0.40
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs3190; hg19: chr2-29025479;