rs782586

chr2-55609029-A-C

Variant summary

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

The NM_001122964.3(PPP4R3B):c.199-4953T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,994 control chromosomes in the GnomAD database, including 15,914 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 (15914 hom., cov: 32)
• Consequence: PPP4R3B NM_001122964.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

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=-0.88).
• 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	UniProt
PPP4R3B	NM_001122964.3	c.199-4953T>G		intron_variant		ENST00000616407.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP4R3B	ENST00000616407.2	c.199-4953T>G		intron_variant		1	NM_001122964.3
PPP4R3B	ENST00000611717.4	c.199-4953T>G		intron_variant		1
PPP4R3B	ENST00000616288.4	c.199-4953T>G		intron_variant		1		P1
PPP4R3B	ENST00000470801.1	n.157-4953T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67340 AN: 151876 Hom.: 15914 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.443 AC: 67361 AN: 151994 Hom.: 15914 Cov.: 32 AF XY: 0.441 AC XY: 32752 AN XY: 74300

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.471

Alfa AF: 0.477 Hom.: 6918

Bravo AF: 0.432

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.63

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: rs782586; hg19: chr2-55836165;