rs9532

chr17-39636360-G-Achr17-39636360-G-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

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]

LOC124903998 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PPP1R1B	NM_032192.4	c.*495G>A		3_prime_UTR_variant	7/7	ENST00000254079.9
LOC124903998	XR_007065749.1	n.300+631C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R1B	ENST00000254079.9	c.*495G>A		3_prime_UTR_variant	7/7	1	NM_032192.4	P1

Frequencies

GnomAD3 genomes AF: 0.0386 AC: 5870 AN: 152096 Hom.: 176 Cov.: 32

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: 65 AN: 2786 Hom.: 3 Cov.: 0 AF XY: 0.0269 AC XY: 41 AN XY: 1526

Gnomad4 AFR exome AF: 0.0750

Gnomad4 AMR exome AF: 0.0191

Gnomad4 ASJ exome AF: 0.0333

Gnomad4 EAS exome AF: 0.0227

Gnomad4 SAS exome AF: 0.0318

Gnomad4 FIN exome AF: 0.0408

Gnomad4 NFE exome AF: 0.0171

Gnomad4 OTH exome AF: 0.00926

GnomAD4 genome AF: 0.0387 AC: 5887 AN: 152214 Hom.: 176 Cov.: 32 AF XY: 0.0386 AC XY: 2875 AN XY: 74434

Gnomad4 AFR AF: 0.0821

Gnomad4 AMR AF: 0.0284

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0369

Gnomad4 FIN AF: 0.0261

Gnomad4 NFE AF: 0.0208

Gnomad4 OTH AF: 0.0317

Alfa AF: 0.0246 Hom.: 74

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
Dann	Benign	0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9532; hg19: chr17-37792613;