2-28783757-GAAAA-GAAA

Variant names:

• chr2-28783757-GA-G
• rs11449670
• NM_002709.3:c.521-138delA

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_002709.3(PPP1CB):​c.521-138delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0745 in 453,292 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0011 (1 hom., cov: 28)
  • Exomes 𝑓: 0.11 (0 hom.)
• Consequence: PPP1CB NM_002709.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 0 publications found

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:30613): (speedy/RINGO cell cycle regulator family member A) Enables protein kinase activator activity and protein kinase binding activity. Involved in several processes, including G1/S transition of mitotic cell cycle; positive regulation of cell population proliferation; and positive regulation of protein kinase activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 148 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1CB	NM_002709.3	c.521-138delA		intron_variant	Intron 4 of 7	ENST00000395366.3	NP_002700.1
PPP1CB	NM_206876.2	c.521-138delA		intron_variant	Intron 5 of 8		NP_996759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1CB	ENST00000395366.3	c.521-149delA		intron_variant	Intron 4 of 7	1	NM_002709.3	ENSP00000378769.2

Frequencies

GnomAD3 genomes AF: 0.00104 AC: 147 AN: 140876 Hom.: 1 Cov.: 28

Gnomad AFR AF: 0.00235

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000642

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000205

Gnomad SAS AF: 0.000220

Gnomad FIN AF: 0.00211

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000404

Gnomad OTH AF: 0.00105

GnomAD4 exome AF: 0.108 AC: 33639 AN: 312368 Hom.: 0 AF XY: 0.107 AC XY: 17817 AN XY: 166300

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0775 AC: 663 AN: 8554

American (AMR) AF: 0.120 AC: 1603 AN: 13328

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 977 AN: 8730

East Asian (EAS) AF: 0.101 AC: 2070 AN: 20542

South Asian (SAS) AF: 0.111 AC: 3351 AN: 30302

European-Finnish (FIN) AF: 0.102 AC: 1990 AN: 19518

Middle Eastern (MID) AF: 0.108 AC: 134 AN: 1240

European-Non Finnish (NFE) AF: 0.109 AC: 21006 AN: 193018

Other (OTH) AF: 0.108 AC: 1845 AN: 17136

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.00105 AC: 148 AN: 140924 Hom.: 1 Cov.: 28 AF XY: 0.00106 AC XY: 72 AN XY: 68034

African (AFR) AF: 0.00235 AC: 91 AN: 38750

American (AMR) AF: 0.000641 AC: 9 AN: 14034

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3312

East Asian (EAS) AF: 0.000206 AC: 1 AN: 4860

South Asian (SAS) AF: 0.000442 AC: 2 AN: 4520

European-Finnish (FIN) AF: 0.00211 AC: 17 AN: 8038

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 272

European-Non Finnish (NFE) AF: 0.000404 AC: 26 AN: 64328

Other (OTH) AF: 0.00104 AC: 2 AN: 1926

Alfa AF: 0.0000762 Hom.: 17

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism

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: rs11449670; hg19: chr2-29006623;