rs10496050

chr2-55579177-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.1468+502G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,886 control chromosomes in the GnomAD database, including 16,060 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 (16060 hom., cov: 32)
• Consequence: PPP4R3B NM_001122964.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP4R3B	NM_001122964.3	c.1468+502G>A		intron_variant		ENST00000616407.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP4R3B	ENST00000616407.2	c.1468+502G>A		intron_variant		1	NM_001122964.3
PPP4R3B	ENST00000611717.4	c.1468+502G>A		intron_variant		1
PPP4R3B	ENST00000616288.4	c.1468+502G>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67926 AN: 151766 Hom.: 16061 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.447 AC: 67950 AN: 151886 Hom.: 16060 Cov.: 32 AF XY: 0.445 AC XY: 33055 AN XY: 74216

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.476

Alfa AF: 0.488 Hom.: 8358

Bravo AF: 0.437

Asia WGS AF: 0.276 AC: 960 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.028
Dann	Benign	0.61

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: rs10496050; hg19: chr2-55806313;