rs7072006

Positions:

• chr10-131932124-C-T

Variant summary

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

The ENST00000455566.6(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 ENST00000455566.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP2R2D	NM_018461.5	c.101-2334C>T		intron_variant		ENST00000455566.6	NP_060931.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP2R2D	ENST00000455566.6	c.101-2334C>T		intron_variant		1	NM_018461.5	ENSP00000399970	P1
PPP2R2D	ENST00000470416.5	c.*904-2334C>T		intron_variant, NMD_transcript_variant		1		ENSP00000485636
PPP2R2D	ENST00000616467.4	c.101-2334C>T		intron_variant, NMD_transcript_variant		1		ENSP00000481133
PPP2R2D	ENST00000482010.6	c.66-2334C>T		intron_variant, NMD_transcript_variant		2		ENSP00000428418

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

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.0556

Gnomad4 FIN AF: 0.0758

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.152

Alfa AF: 0.140 Hom.: 2876

Bravo AF: 0.159

Asia WGS AF: 0.0540 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.86
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

Publications

LitVar

Other links and lift over

dbSNP: rs7072006; hg19: chr10-133745628;