Variant rs3748140 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024607.4(PPP1R3B):c.143G>A(p.Gly48Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 1,614,174 control chromosomes in the GnomAD database, including 1,225 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.026 ( 139 hom., cov: 32)

Exomes 𝑓: 0.020 ( 1086 hom. )

Consequence

PPP1R3B
NM_024607.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.51

Variant links:

Genes affected

PPP1R3B (HGNC:14942): (protein phosphatase 1 regulatory subunit 3B) This gene encodes the catalytic subunit of the serine/theonine phosphatase, protein phosphatase-1. The encoded protein is expressed in liver and skeletal muscle tissue and may be involved in regulating glycogen synthesis in these tissues. This gene may be a involved in type 2 diabetes and maturity-onset diabetes of the young. Alternate splicing results in multiple transcript variants that encode the same protein.[provided by RefSeq, Jan 2011]

PPP1R3B links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0014359355).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP1R3B	NM_024607.4 linkuse as main transcript	c.143G>A	p.Gly48Glu	missense_variant	2/2	ENST00000310455.4	NP_078883.2
LOC124901882	XR_007060810.1 linkuse as main transcript	n.91C>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R3B	ENST00000310455.4 linkuse as main transcript	c.143G>A	p.Gly48Glu	missense_variant	2/2	1	NM_024607.4	ENSP00000308318	P1
	ENST00000666082.1 linkuse as main transcript	n.83C>T		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes

AF:

0.0256

AC:

3890

AN:

152168

Hom.:

139

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0411

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0137

Gnomad ASJ

AF:

0.00548

Gnomad EAS

AF:

0.0709

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.0143

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0104

Gnomad OTH

AF:

0.0224

GnomAD3 exomes

AF:

0.0311

AC:

7816

AN:

251446

Hom.:

353

AF XY:

0.0349

AC XY:

4738

AN XY:

135896

show subpopulations

Gnomad AFR exome

AF:

0.0418

Gnomad AMR exome

AF:

0.0103

Gnomad ASJ exome

AF:

0.00526

Gnomad EAS exome

AF:

0.0626

Gnomad SAS exome

AF:

0.129

Gnomad FIN exome

AF:

0.0114

Gnomad NFE exome

AF:

0.0110

Gnomad OTH exome

AF:

0.0231

GnomAD4 exome

AF:

0.0204

AC:

29835

AN:

1461888

Hom.:

1086

Cov.:

AF XY:

0.0233

AC XY:

16940

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.0434

Gnomad4 AMR exome

AF:

0.0111

Gnomad4 ASJ exome

AF:

0.00425

Gnomad4 EAS exome

AF:

0.0741

Gnomad4 SAS exome

AF:

0.127

Gnomad4 FIN exome

AF:

0.0113

Gnomad4 NFE exome

AF:

0.0104

Gnomad4 OTH exome

AF:

0.0262

GnomAD4 genome

AF:

0.0256

AC:

3899

AN:

152286

Hom.:

139

Cov.:

AF XY:

0.0280

AC XY:

2087

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0410

Gnomad4 AMR

AF:

0.0137

Gnomad4 ASJ

AF:

0.00548

Gnomad4 EAS

AF:

0.0711

Gnomad4 SAS

AF:

0.141

Gnomad4 FIN

AF:

0.0143

Gnomad4 NFE

AF:

0.0104

Gnomad4 OTH

AF:

0.0232

Alfa

AF:

0.0144

Hom.:

Bravo

AF:

0.0224

TwinsUK

AF:

0.00971

AC:

ALSPAC

AF:

0.00778

AC:

ESP6500AA

AF:

0.0420

AC:

185

ESP6500EA

AF:

0.0107

AC:

ExAC

AF:

0.0334

AC:

4058

Asia WGS

AF:

0.107

AC:

370

AN:

3478

EpiCase

AF:

0.0105

EpiControl

AF:

0.0133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.091

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.86

DEOGEN2

Benign

0.032

T;T

Eigen

Benign

-0.42

Eigen_PC

Benign

-0.33

FATHMM_MKL

Benign

0.65

MetaRNN

Benign

0.0014

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.60

N;N

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.49

PROVEAN

Benign

-0.20

N;N

REVEL

Benign

0.058

Sift

Benign

0.46

T;T

Sift4G

Benign

0.88

T;T

Polyphen

0.0030

B;B

Vest4

0.038

MPC

0.049

ClinPred

0.0096

GERP RS

5.8

Varity_R

0.11

gMVP

0.33

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over