chr10-131956344-C-G

Position:

• chr10-131956344-C-G

Variant summary

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

The ENST00000455566.6(PPP2R2D):​c.*381C>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 0.25 in 988,370 control chromosomes in the GnomAD database, including 31,315 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 0.28 (6028 hom., cov: 33)
  • Exomes 𝑓: 0.24 (25287 hom.)
• Consequence: PPP2R2D ENST00000455566.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

PPP2R2D (HGNC:23732): (protein phosphatase 2 regulatory subunit Bdelta) Predicted to enable protein phosphatase regulator activity. Predicted to be involved in exit from mitosis and peptidyl-serine dephosphorylation. Predicted to be part of protein phosphatase type 2A complex. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP2R2D	NM_018461.5	c.*381C>G		3_prime_UTR_variant	9/9	ENST00000455566.6	NP_060931.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP2R2D	ENST00000455566.6	c.*381C>G		3_prime_UTR_variant	9/9	1	NM_018461.5	ENSP00000399970	P1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42398 AN: 151966 Hom.: 6019 Cov.: 33

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.278

GnomAD4 exome AF: 0.245 AC: 204718 AN: 836286 Hom.: 25287 Cov.: 30 AF XY: 0.244 AC XY: 94374 AN XY: 386304

Gnomad4 AFR exome AF: 0.291

Gnomad4 AMR exome AF: 0.280

Gnomad4 ASJ exome AF: 0.342

Gnomad4 EAS exome AF: 0.473

Gnomad4 SAS exome AF: 0.279

Gnomad4 FIN exome AF: 0.238

Gnomad4 NFE exome AF: 0.240

Gnomad4 OTH exome AF: 0.263

GnomAD4 genome AF: 0.279 AC: 42444 AN: 152084 Hom.: 6028 Cov.: 33 AF XY: 0.281 AC XY: 20915 AN XY: 74326

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.278

Alfa AF: 0.140 Hom.: 252

Bravo AF: 0.283

Asia WGS AF: 0.339 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.78
DANN	Benign	0.60
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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: rs7199; hg19: chr10-133769848; COSMIC: COSV70778750; COSMIC: COSV70778750;