rs782588

Positions:

• chr2-55614504-T-C

Variant summary

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

The NM_001122964.3(PPP4R3B):​c.198+947A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 152,036 control chromosomes in the GnomAD database, including 16,250 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 0.45 (16250 hom., cov: 34)
  • Failed GnomAD Quality Control
• Consequence: PPP4R3B NM_001122964.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP4R3B	NM_001122964.3	c.198+947A>G		intron_variant		ENST00000616407.2	NP_001116436.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP4R3B	ENST00000616407.2	c.198+947A>G		intron_variant		1	NM_001122964.3	ENSP00000483228

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68337 AN: 151918 Hom.: 16250 Cov.: 34

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.478

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.450 AC: 68358 AN: 152036 Hom.: 16250 Cov.: 34 AF XY: 0.447 AC XY: 33233 AN XY: 74334

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.475

Alfa AF: 0.486 Hom.: 8420

Bravo AF: 0.440

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.71
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs782588; hg19: chr2-55841640;