dbSNP rs2271309: PPP1R1B:c.82-433G>A (chr17-39628737-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.82-433G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 994,260 control chromosomes in the GnomAD database, including 285,255 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 ( 31457 hom., cov: 33)

Exomes 𝑓: 0.77 ( 253798 hom. )

Consequence

PPP1R1B
NM_032192.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

14 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R1B	NM_032192.4 link	c.82-433G>A		intron_variant	Intron 1 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.82-433G>A		intron_variant	Intron 1 of 6	1	NM_032192.4	ENSP00000254079.4		Q9UD71-1

Frequencies

GnomAD3 genomes

AF:

0.605

AC:

91924

AN:

152058

Hom.:

31450

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.746

Gnomad AMR

AF:

0.613

Gnomad ASJ

AF:

0.739

Gnomad EAS

AF:

0.441

Gnomad SAS

AF:

0.722

Gnomad FIN

AF:

0.778

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.769

Gnomad OTH

AF:

0.634

GnomAD4 exome

AF:

0.772

AC:

650182

AN:

842084

Hom.:

253798

Cov.:

AF XY:

0.773

AC XY:

301502

AN XY:

389982

show subpopulations

African (AFR)

AF:

0.252

AC:

3985

AN:

15790

American (AMR)

AF:

0.641

AC:

1343

AN:

2094

Ashkenazi Jewish (ASJ)

AF:

0.736

AC:

3953

AN:

5374

East Asian (EAS)

AF:

0.433

AC:

1665

AN:

3844

South Asian (SAS)

AF:

0.758

AC:

13791

AN:

18182

European-Finnish (FIN)

AF:

0.785

AC:

634

AN:

808

Middle Eastern (MID)

AF:

0.788

AC:

1314

AN:

1668

European-Non Finnish (NFE)

AF:

0.787

AC:

603113

AN:

766554

Other (OTH)

AF:

0.734

AC:

20384

AN:

27770

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

7078

14156

21235

28313

35391

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19168

38336

57504

76672

95840

<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:

0.604

AC:

91952

AN:

152176

Hom.:

31457

Cov.:

AF XY:

0.603

AC XY:

44893

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.276

AC:

11474

AN:

41514

American (AMR)

AF:

0.613

AC:

9387

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.739

AC:

2567

AN:

3472

East Asian (EAS)

AF:

0.441

AC:

2280

AN:

5170

South Asian (SAS)

AF:

0.722

AC:

3486

AN:

4826

European-Finnish (FIN)

AF:

0.778

AC:

8253

AN:

10602

Middle Eastern (MID)

AF:

0.707

AC:

208

AN:

294

European-Non Finnish (NFE)

AF:

0.769

AC:

52277

AN:

67970

Other (OTH)

AF:

0.634

AC:

1341

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1551

3102

4652

6203

7754

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

744

1488

2232

2976

3720

<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:

0.650

Hom.:

4525

Bravo

AF:

0.577

Asia WGS

AF:

0.607

AC:

2112

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.18

(source)

DANN

Benign

0.56

PhyloP100

-1.0

PromoterAI

0.0041

Neutral

(source)

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