rs7074421

Variant names:

• chr10-131933994-G-A
• rs7074421
• NM_018461.5:c.101-464G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-131933994-G-A
• chr10-131933994-G-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.101-464G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,046 control chromosomes in the GnomAD database, including 1,897 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 (1897 hom., cov: 32)
• Consequence: PPP2R2D NM_018461.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• 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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP2R2D	NM_018461.5	c.101-464G>A		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.101-464G>A		intron_variant	Intron 2 of 8	1	NM_018461.5	ENSP00000399970.2
PPP2R2D	ENST00000470416.5	n.*904-464G>A		intron_variant	Intron 2 of 8	1		ENSP00000485636.1
PPP2R2D	ENST00000616467.4	n.101-464G>A		intron_variant	Intron 2 of 9	1		ENSP00000481133.2
PPP2R2D	ENST00000482010.6	n.65-464G>A		intron_variant	Intron 1 of 7	2		ENSP00000428418.2

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22699 AN: 151930 Hom.: 1890 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0205

Gnomad SAS AF: 0.0551

Gnomad FIN AF: 0.0764

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.150 AC: 22731 AN: 152046 Hom.: 1897 Cov.: 32 AF XY: 0.143 AC XY: 10661 AN XY: 74342

African (AFR) AF: 0.215 AC: 8897 AN: 41432

American (AMR) AF: 0.122 AC: 1862 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3472

East Asian (EAS) AF: 0.0203 AC: 105 AN: 5168

South Asian (SAS) AF: 0.0560 AC: 270 AN: 4824

European-Finnish (FIN) AF: 0.0764 AC: 807 AN: 10562

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.144 AC: 9822 AN: 67984

Other (OTH) AF: 0.152 AC: 321 AN: 2114

Alfa AF: 0.0926 Hom.: 177

Bravo AF: 0.157

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.3
DANN	Benign	0.76
PhyloP100		-0.065

Splicing

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

Other links and lift over

dbSNP: rs7074421; hg19: chr10-133747498;