rs782590

chr2-55616277-C-T

Variant summary

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

The NM_001122964.3(PPP4R3B):c.143-771G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151,908 control chromosomes in the GnomAD database, including 15,636 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 0.44 (15636 hom., cov: 30)
• Consequence: PPP4R3B NM_001122964.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

Genes affected

PPP4R3B (HGNC:29267): (protein phosphatase 4 regulatory subunit 3B) Predicted to act upstream of or within positive regulation of gluconeogenesis and protein dephosphorylation. Located in centrosome and nuclear speck. [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=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP4R3B	NM_001122964.3	c.143-771G>A		intron_variant		ENST00000616407.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP4R3B	ENST00000616407.2	c.143-771G>A		intron_variant		1	NM_001122964.3

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66825 AN: 151788 Hom.: 15637 Cov.: 30

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.440 AC: 66843 AN: 151908 Hom.: 15636 Cov.: 30 AF XY: 0.438 AC XY: 32544 AN XY: 74234

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.467

Alfa AF: 0.488 Hom.: 13572

Bravo AF: 0.428

Asia WGS AF: 0.234 AC: 812 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	10
Dann	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs782590; hg19: chr2-55843413;