dbSNP rs907094: PPP1R1B:c.445+32G>A (chr17-39634118-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_032192.4(PPP1R1B):c.445+32G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 1,611,418 control chromosomes in the GnomAD database, including 452,561 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 0.60 ( 31345 hom., cov: 32)

Exomes 𝑓: 0.75 ( 421216 hom. )

Consequence

PPP1R1B
NM_032192.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76

Publications

64 publications found

Variant links:

Genes affected

PPP1R1B (HGNC:9287): (protein phosphatase 1 regulatory inhibitor subunit 1B) This gene encodes a bifunctional signal transduction molecule. Dopaminergic and glutamatergic receptor stimulation regulates its phosphorylation and function as a kinase or phosphatase inhibitor. As a target for dopamine, this gene may serve as a therapeutic target for neurologic and psychiatric disorders. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

PPP1R1B 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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R1B	NM_032192.4 link	c.445+32G>A		intron_variant	Intron 5 of 6	ENST00000254079.9	NP_115568.2	Q9UD71-1B3KVQ9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R1B	ENST00000254079.9 link	c.445+32G>A		intron_variant	Intron 5 of 6	1	NM_032192.4	ENSP00000254079.4		Q9UD71-1

Frequencies

GnomAD3 genomes

AF:

0.603

AC:

91624

AN:

151974

Hom.:

31340

Cov.:

show subpopulations

Gnomad AFR

AF:

0.272

Gnomad AMI

AF:

0.747

Gnomad AMR

AF:

0.611

Gnomad ASJ

AF:

0.738

Gnomad EAS

AF:

0.444

Gnomad SAS

AF:

0.722

Gnomad FIN

AF:

0.778

Gnomad MID

AF:

0.718

Gnomad NFE

AF:

0.768

Gnomad OTH

AF:

0.634

GnomAD2 exomes

AF:

0.694

AC:

173419

AN:

249982

AF XY:

0.711

show subpopulations

Gnomad AFR exome

AF:

0.260

Gnomad AMR exome

AF:

0.640

Gnomad ASJ exome

AF:

0.746

Gnomad EAS exome

AF:

0.415

Gnomad FIN exome

AF:

0.784

Gnomad NFE exome

AF:

0.779

Gnomad OTH exome

AF:

0.731

GnomAD4 exome

AF:

0.753

AC:

1099022

AN:

1459326

Hom.:

421216

Cov.:

AF XY:

0.755

AC XY:

547981

AN XY:

725876

show subpopulations

African (AFR)

AF:

0.261

AC:

8717

AN:

33426

American (AMR)

AF:

0.636

AC:

28433

AN:

44698

Ashkenazi Jewish (ASJ)

AF:

0.741

AC:

19355

AN:

26120

East Asian (EAS)

AF:

0.481

AC:

19095

AN:

39680

South Asian (SAS)

AF:

0.758

AC:

65277

AN:

86146

European-Finnish (FIN)

AF:

0.780

AC:

41242

AN:

52844

Middle Eastern (MID)

AF:

0.766

AC:

3913

AN:

5110

European-Non Finnish (NFE)

AF:

0.783

AC:

869567

AN:

1111036

Other (OTH)

AF:

0.721

AC:

43423

AN:

60266

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

12731

25461

38192

50922

63653

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20384

40768

61152

81536

101920

<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:

0.603

AC:

91647

AN:

152092

Hom.:

31345

Cov.:

AF XY:

0.602

AC XY:

44765

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.272

AC:

11284

AN:

41486

American (AMR)

AF:

0.612

AC:

9347

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.738

AC:

2560

AN:

3468

East Asian (EAS)

AF:

0.444

AC:

2293

AN:

5166

South Asian (SAS)

AF:

0.723

AC:

3487

AN:

4822

European-Finnish (FIN)

AF:

0.778

AC:

8239

AN:

10594

Middle Eastern (MID)

AF:

0.718

AC:

211

AN:

294

European-Non Finnish (NFE)

AF:

0.768

AC:

52208

AN:

67962

Other (OTH)

AF:

0.634

AC:

1337

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1497

2994

4491

5988

7485

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

742

1484

2226

2968

3710

<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:

0.711

Hom.:

112626

Bravo

AF:

0.575

Asia WGS

AF:

0.610

AC:

2123

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.6

(source)

DANN

Benign

0.67

PhyloP100

-1.8

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over