dbSNP rs9532: PPP1R1B:c.*495G>A (chr17-39636360-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.*495G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0384 in 155,000 control chromosomes in the GnomAD database, including 179 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 0.039 ( 176 hom., cov: 32)

Exomes 𝑓: 0.023 ( 3 hom. )

Consequence

PPP1R1B
NM_032192.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0270

Publications

4 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:

ENSG00000306162 (HGNC:):

ENSG00000306162 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=-0.73).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0798 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032192.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PPP1R1B	NM_032192.4	MANE Select	c.*495G>A	3_prime_UTR	Exon 7 of 7	NP_115568.2
PPP1R1B	NM_001242464.2		c.*495G>A	3_prime_UTR	Exon 7 of 7	NP_001229393.1
PPP1R1B	NM_181505.4		c.*495G>A	3_prime_UTR	Exon 7 of 7	NP_852606.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PPP1R1B	ENST00000254079.9	TSL:1 MANE Select	c.*495G>A	3_prime_UTR	Exon 7 of 7	ENSP00000254079.4
PPP1R1B	ENST00000394265.5	TSL:1	c.*495G>A	3_prime_UTR	Exon 7 of 7	ENSP00000377808.1
PPP1R1B	ENST00000394267.2	TSL:1	c.*495G>A	3_prime_UTR	Exon 7 of 7	ENSP00000377810.2

Frequencies

GnomAD3 genomes

AF:

0.0386

AC:

5870

AN:

152096

Hom.:

176

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0819

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.0285

Gnomad ASJ

AF:

0.0179

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.0373

Gnomad FIN

AF:

0.0261

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0208

Gnomad OTH

AF:

0.0320

GnomAD4 exome

AF:

0.0233

AC:

AN:

2786

Hom.:

Cov.:

AF XY:

0.0269

AC XY:

AN XY:

1526

show subpopulations

African (AFR)

AF:

0.0750

AC:

AN:

American (AMR)

AF:

0.0191

AC:

AN:

262

Ashkenazi Jewish (ASJ)

AF:

0.0333

AC:

AN:

East Asian (EAS)

AF:

0.0227

AC:

AN:

176

South Asian (SAS)

AF:

0.0318

AC:

AN:

314

European-Finnish (FIN)

AF:

0.0408

AC:

AN:

392

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0171

AC:

AN:

1462

Other (OTH)

AF:

0.00926

AC:

AN:

108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.533

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.0387

AC:

5887

AN:

152214

Hom.:

176

Cov.:

AF XY:

0.0386

AC XY:

2875

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.0821

AC:

3410

AN:

41514

American (AMR)

AF:

0.0284

AC:

435

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0179

AC:

AN:

3472

East Asian (EAS)

AF:

0.00232

AC:

AN:

5180

South Asian (SAS)

AF:

0.0369

AC:

178

AN:

4826

European-Finnish (FIN)

AF:

0.0261

AC:

276

AN:

10594

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0208

AC:

1417

AN:

68014

Other (OTH)

AF:

0.0317

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

264

528

791

1055

1319

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

192

256

320

<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:

0.0269

Hom.:

117

Bravo

AF:

0.0398

Asia WGS

AF:

0.0320

AC:

111

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

8.0

(source)

DANN

Benign

0.77

PhyloP100

-0.027

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over