rs9419202

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-131933260-C-G
• chr10-131933260-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018461.5(PPP2R2D):​c.101-1198C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: PPP2R2D NM_018461.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP2R2D	NM_018461.5	c.101-1198C>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.101-1198C>G		intron_variant	Intron 2 of 8	1	NM_018461.5	ENSP00000399970.2
PPP2R2D	ENST00000470416.5	n.*904-1198C>G		intron_variant	Intron 2 of 8	1		ENSP00000485636.1
PPP2R2D	ENST00000616467.4	n.101-1198C>G		intron_variant	Intron 2 of 9	1		ENSP00000481133.2
PPP2R2D	ENST00000482010.6	n.65-1198C>G		intron_variant	Intron 1 of 7	2		ENSP00000428418.2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.023
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9419202; hg19: chr10-133746764;