chr10-131932772-A-G

Variant names:

• chr10-131932772-A-G
• rs11146169
• NM_018461.5:c.101-1686A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS1

The NM_018461.5(PPP2R2D):​c.101-1686A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000773 in 151,402 control chromosomes in the GnomAD database, including 1 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 0.00077 (1 hom., cov: 31)
• Consequence: PPP2R2D NM_018461.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.000773 (117/151402) while in subpopulation EAS AF = 0.0209 (108/5172). AF 95% confidence interval is 0.0177. There are 1 homozygotes in GnomAd4. There are 73 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP2R2D	NM_018461.5	c.101-1686A>G		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.101-1686A>G		intron_variant	Intron 2 of 8	1	NM_018461.5	ENSP00000399970.2
PPP2R2D	ENST00000470416.5	n.*904-1686A>G		intron_variant	Intron 2 of 8	1		ENSP00000485636.1
PPP2R2D	ENST00000616467.4	n.101-1686A>G		intron_variant	Intron 2 of 9	1		ENSP00000481133.2
PPP2R2D	ENST00000482010.6	n.65-1686A>G		intron_variant	Intron 1 of 7	2		ENSP00000428418.2

Frequencies

GnomAD3 genomes AF: 0.000773 AC: 117 AN: 151296 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.00125

Gnomad FIN AF: 0.0000961

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.000484

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

GnomAD4 genome AF: 0.000773 AC: 117 AN: 151402 Hom.: 1 Cov.: 31 AF XY: 0.000987 AC XY: 73 AN XY: 73994

African (AFR) AF: 0.00 AC: 0 AN: 41370

American (AMR) AF: 0.00 AC: 0 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3410

East Asian (EAS) AF: 0.0209 AC: 108 AN: 5172

South Asian (SAS) AF: 0.00125 AC: 6 AN: 4794

European-Finnish (FIN) AF: 0.0000961 AC: 1 AN: 10406

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 67822

Other (OTH) AF: 0.000480 AC: 1 AN: 2084

Alfa AF: 0.000598 Hom.: 0

Bravo AF: 0.00123

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.46
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs11146169; hg19: chr10-133746276;