rs77523588

Variant names:

• chr10-131932846-A-T
• rs77523588
• NM_018461.5:c.101-1612A>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.101-1612A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00299 in 152,088 control chromosomes in the GnomAD database, including 21 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 0.0030 (21 hom., cov: 31)
• Consequence: PPP2R2D NM_018461.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP2R2D	NM_018461.5	c.101-1612A>T		intron_variant	Intron 2 of 8	ENST00000455566.6	NP_060931.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP2R2D	ENST00000455566.6	c.101-1612A>T		intron_variant	Intron 2 of 8	1	NM_018461.5	ENSP00000399970.2
PPP2R2D	ENST00000470416.5	n.*904-1612A>T		intron_variant	Intron 2 of 8	1		ENSP00000485636.1
PPP2R2D	ENST00000616467.4	n.101-1612A>T		intron_variant	Intron 2 of 9	1		ENSP00000481133.2
PPP2R2D	ENST00000482010.6	n.65-1612A>T		intron_variant	Intron 1 of 7	2		ENSP00000428418.2

Frequencies

GnomAD3 genomes AF: 0.00299 AC: 454 AN: 151970 Hom.: 20 Cov.: 31

Gnomad AFR AF: 0.0000967

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000328

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.00352

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000735

Gnomad OTH AF: 0.00335

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

GnomAD4 genome AF: 0.00299 AC: 454 AN: 152088 Hom.: 21 Cov.: 31 AF XY: 0.00343 AC XY: 255 AN XY: 74356

African (AFR) AF: 0.0000964 AC: 4 AN: 41482

American (AMR) AF: 0.000327 AC: 5 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3468

East Asian (EAS) AF: 0.0790 AC: 408 AN: 5166

South Asian (SAS) AF: 0.00353 AC: 17 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10566

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000735 AC: 5 AN: 67994

Other (OTH) AF: 0.00426 AC: 9 AN: 2112

Alfa AF: 0.00111 Hom.: 0

Bravo AF: 0.00374

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.50
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs77523588; hg19: chr10-133746350;