rs782586

Variant names:

• chr2-55609029-A-C
• rs782586
• NM_001122964.3:c.199-4953T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001122964.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP4R3B	NM_001122964.3	MANE Select	c.199-4953T>G		intron	N/A	NP_001116436.3
	PPP4R3B	NM_001282850.2		c.199-4953T>G		intron	N/A	NP_001269779.1
	PPP4R3B	NM_020463.4		c.199-4953T>G		intron	N/A	NP_065196.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP4R3B	ENST00000616407.2	TSL:1 MANE Select	c.199-4953T>G		intron	N/A	ENSP00000483228.1
	PPP4R3B	ENST00000616288.4	TSL:1	c.199-4953T>G		intron	N/A	ENSP00000484116.1
	PPP4R3B	ENST00000611717.4	TSL:1	c.199-4953T>G		intron	N/A	ENSP00000478677.1

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

African (AFR) AF: 0.326 AC: 13527 AN: 41470

American (AMR) AF: 0.492 AC: 7514 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3470

East Asian (EAS) AF: 0.109 AC: 564 AN: 5172

South Asian (SAS) AF: 0.260 AC: 1252 AN: 4814

European-Finnish (FIN) AF: 0.576 AC: 6074 AN: 10548

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.521 AC: 35404 AN: 67958

Other (OTH) AF: 0.471 AC: 993 AN: 2108

Alfa AF: 0.456 Hom.: 8723

Bravo AF: 0.432

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		0.054

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

Other links and lift over

dbSNP: rs782586; hg19: chr2-55836165;