10-131933260-C-T

Variant names:

• chr10-131933260-C-T
• rs9419202
• NM_018461.5:c.101-1198C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018461.5(PPP2R2D):​c.101-1198C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,162 control chromosomes in the GnomAD database, including 1,891 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 0.15 (1891 hom., cov: 32)
• Consequence: PPP2R2D NM_018461.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018461.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP2R2D	NM_018461.5	MANE Select	c.101-1198C>T		intron	N/A	NP_060931.2
	PPP2R2D	NM_001291310.2		c.-395-1198C>T		intron	N/A	NP_001278239.1
	PPP2R2D	NR_033191.3		n.242-1198C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP2R2D	ENST00000455566.6	TSL:1 MANE Select	c.101-1198C>T		intron	N/A	ENSP00000399970.2
	PPP2R2D	ENST00000470416.5	TSL:1	n.*904-1198C>T		intron	N/A	ENSP00000485636.1
	PPP2R2D	ENST00000616467.4	TSL:1	n.101-1198C>T		intron	N/A	ENSP00000481133.2

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22696 AN: 152044 Hom.: 1884 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.0555

Gnomad FIN AF: 0.0761

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.154

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.149 AC: 22728 AN: 152162 Hom.: 1891 Cov.: 32 AF XY: 0.143 AC XY: 10644 AN XY: 74402

African (AFR) AF: 0.215 AC: 8897 AN: 41464

American (AMR) AF: 0.122 AC: 1860 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3470

East Asian (EAS) AF: 0.0206 AC: 107 AN: 5186

South Asian (SAS) AF: 0.0563 AC: 272 AN: 4828

European-Finnish (FIN) AF: 0.0761 AC: 807 AN: 10606

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9817 AN: 67996

Other (OTH) AF: 0.152 AC: 321 AN: 2112

Alfa AF: 0.102 Hom.: 230

Bravo AF: 0.157

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.053
DANN	Benign	0.75
PhyloP100		-0.95

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9419202; hg19: chr10-133746764;