dbSNP rs330919: PPP1R3B:c.*889C>T (chr8-9139905-G-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.*889C>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 0.291 in 152,024 control chromosomes in the GnomAD database, including 7,667 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 0.29 ( 7666 hom., cov: 32)

Exomes 𝑓: 0.17 ( 1 hom. )

Consequence

PPP1R3B
NM_024607.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.14

Publications

11 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=-0.56).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PPP1R3B	NM_024607.4 link	c.*889C>T	3_prime_UTR_variant	Exon 2 of 2	ENST00000310455.4	NP_078883.2	Q86XI6
PPP1R3B	NM_001201329.2 link	c.*889C>T	3_prime_UTR_variant	Exon 2 of 2		NP_001188258.1	Q86XI6
PPP1R3B	XM_006716253.4 link	c.*889C>T	3_prime_UTR_variant	Exon 2 of 2		XP_006716316.1	Q86XI6
PPP1R3B	XM_047422235.1 link	c.*889C>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.*889C>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_024607.4	ENSP00000308318.3		Q86XI6
PPP1R3B	ENST00000519699.1 link	c.*889C>T		3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000428642.1		Q86XI6

Frequencies

GnomAD3 genomes

AF:

0.291

AC:

44186

AN:

151888

Hom.:

7672

Cov.:

show subpopulations

Gnomad AFR

AF:

0.167

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.279

Gnomad EAS

AF:

0.753

Gnomad SAS

AF:

0.540

Gnomad FIN

AF:

0.247

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.297

Gnomad OTH

AF:

0.325

GnomAD4 exome

AF:

0.167

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0714

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.125

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.291

AC:

44204

AN:

152006

Hom.:

7666

Cov.:

AF XY:

0.298

AC XY:

22137

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.167

AC:

6918

AN:

41468

American (AMR)

AF:

0.390

AC:

5960

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.279

AC:

965

AN:

3460

East Asian (EAS)

AF:

0.753

AC:

3879

AN:

5152

South Asian (SAS)

AF:

0.539

AC:

2596

AN:

4818

European-Finnish (FIN)

AF:

0.247

AC:

2608

AN:

10560

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.297

AC:

20161

AN:

67960

Other (OTH)

AF:

0.326

AC:

687

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1485

2971

4456

5942

7427

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

464

928

1392

1856

2320

<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:

0.306

Hom.:

9420

Bravo

AF:

0.298

Asia WGS

AF:

0.557

AC:

1932

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

9.8

(source)

DANN

Benign

0.79

PhyloP100

2.1

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over