rs907094

chr17-39634118-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PPP1R1B	NM_032192.4	c.445+32G>A		intron_variant		ENST00000254079.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R1B	ENST00000254079.9	c.445+32G>A		intron_variant		1	NM_032192.4	P1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91624 AN: 151974 Hom.: 31340 Cov.: 32

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

GnomAD3 exomes AF: 0.694 AC: 173419 AN: 249982 Hom.: 63184 AF XY: 0.711 AC XY: 96033 AN XY: 135126

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 SAS exome AF: 0.752

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.: 41 AF XY: 0.755 AC XY: 547981 AN XY: 725876

Gnomad4 AFR exome AF: 0.261

Gnomad4 AMR exome AF: 0.636

Gnomad4 ASJ exome AF: 0.741

Gnomad4 EAS exome AF: 0.481

Gnomad4 SAS exome AF: 0.758

Gnomad4 FIN exome AF: 0.780

Gnomad4 NFE exome AF: 0.783

Gnomad4 OTH exome AF: 0.721

GnomAD4 genome AF: 0.603 AC: 91647 AN: 152092 Hom.: 31345 Cov.: 32 AF XY: 0.602 AC XY: 44765 AN XY: 74378

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.634

Alfa AF: 0.744 Hom.: 72801

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
Dann	Benign	0.67

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

LitVar

Other links and lift over

dbSNP: rs907094; hg19: chr17-37790371; COSMIC: COSV54203141; COSMIC: COSV54203141;