NM_018461.5:c.101-2334C>T

Variant names:

• chr10-131932124-C-T
• rs7072006
• NM_018461.5:c.101-2334C>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.101-2334C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,096 control chromosomes in the GnomAD database, including 1,948 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 (1948 hom., cov: 31)
• Consequence: PPP2R2D NM_018461.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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.101-2334C>T		intron	N/A	NP_060931.2
	PPP2R2D	NM_001291310.2		c.-395-2334C>T		intron	N/A	NP_001278239.1
	PPP2R2D	NR_033191.3		n.242-2334C>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.101-2334C>T		intron	N/A	ENSP00000399970.2
	PPP2R2D	ENST00000470416.5	TSL:1	n.*904-2334C>T		intron	N/A	ENSP00000485636.1
	PPP2R2D	ENST00000616467.4	TSL:1	n.101-2334C>T		intron	N/A	ENSP00000481133.2

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22922 AN: 151978 Hom.: 1941 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0201

Gnomad SAS AF: 0.0547

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.111

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: 0.151 AC: 22954 AN: 152096 Hom.: 1948 Cov.: 31 AF XY: 0.145 AC XY: 10771 AN XY: 74346

African (AFR) AF: 0.221 AC: 9144 AN: 41438

American (AMR) AF: 0.123 AC: 1876 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3468

East Asian (EAS) AF: 0.0199 AC: 103 AN: 5172

South Asian (SAS) AF: 0.0556 AC: 268 AN: 4820

European-Finnish (FIN) AF: 0.0758 AC: 803 AN: 10594

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9810 AN: 67994

Other (OTH) AF: 0.152 AC: 321 AN: 2110

Alfa AF: 0.144 Hom.: 6856

Bravo AF: 0.159

Asia WGS AF: 0.0540 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.86
PhyloP100		0.44
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs7072006; hg19: chr10-133745628;