dbSNP rs330915: PPP1R3B:c.*1368A>T (chr8-9139426-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024607.4(PPP1R3B):c.*1368A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,148 control chromosomes in the GnomAD database, including 7,948 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 0.30 ( 7948 hom., cov: 33)

Exomes 𝑓: 0.13 ( 0 hom. )

Consequence

PPP1R3B
NM_024607.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.535

Publications

6 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PPP1R3B	NM_024607.4 link	c.*1368A>T	3_prime_UTR_variant	Exon 2 of 2	ENST00000310455.4	NP_078883.2	Q86XI6
PPP1R3B	NM_001201329.2 link	c.*1368A>T	3_prime_UTR_variant	Exon 2 of 2		NP_001188258.1	Q86XI6
PPP1R3B	XM_006716253.4 link	c.*1368A>T	3_prime_UTR_variant	Exon 2 of 2		XP_006716316.1	Q86XI6
PPP1R3B	XM_047422235.1 link	c.*1368A>T	3_prime_UTR_variant	Exon 2 of 2		XP_047278191.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R3B	ENST00000310455.4 link	c.*1368A>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_024607.4	ENSP00000308318.3		Q86XI6
PPP1R3B	ENST00000519699.1 link	c.*1368A>T		downstream_gene_variant		2		ENSP00000428642.1		Q86XI6

Frequencies

GnomAD3 genomes

AF:

0.300

AC:

45537

AN:

152022

Hom.:

7951

Cov.:

show subpopulations

Gnomad AFR

AF:

0.196

Gnomad AMI

AF:

0.349

Gnomad AMR

AF:

0.399

Gnomad ASJ

AF:

0.279

Gnomad EAS

AF:

0.754

Gnomad SAS

AF:

0.535

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.296

Gnomad OTH

AF:

0.332

GnomAD4 exome

AF:

0.125

AC:

AN:

Hom.:

Cov.:

AF XY:

0.167

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.299

AC:

45563

AN:

152140

Hom.:

7948

Cov.:

AF XY:

0.306

AC XY:

22755

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.196

AC:

8142

AN:

41496

American (AMR)

AF:

0.399

AC:

6108

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.279

AC:

968

AN:

3470

East Asian (EAS)

AF:

0.754

AC:

3902

AN:

5174

South Asian (SAS)

AF:

0.535

AC:

2580

AN:

4826

European-Finnish (FIN)

AF:

0.246

AC:

2606

AN:

10594

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.296

AC:

20125

AN:

67980

Other (OTH)

AF:

0.333

AC:

701

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1532

3064

4595

6127

7659

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.272

Hom.:

769

Bravo

AF:

0.308

Asia WGS

AF:

0.557

AC:

1931

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.1

(source)

DANN

Benign

0.71

PhyloP100

-0.54

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over