Genetic Variant ENST00000492037.5:n.1027G>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 ENST00000492037.5(PPP1R1B):n.1027G>A variant causes a non coding transcript exon 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
ENST00000492037.5 non_coding_transcript_exon

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:

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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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R1B	NM_032192.4 link	c.*495G>A		3_prime_UTR_variant	Exon 7 of 7	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.*495G>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_032192.4	ENSP00000254079.4		Q9UD71-1

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 v4.3

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

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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