rs12601930

chr17-39633179-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The NM_032192.4(PPP1R1B):c.242-704C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0182 in 153,560 control chromosomes in the GnomAD database, including 209 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 0.018 (206 hom., cov: 32)
  • Exomes 𝑓: 0.013 (3 hom.)
• Consequence: PPP1R1B NM_032192.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64

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 -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.12).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP1R1B	NM_032192.4	c.242-704C>T		intron_variant		ENST00000254079.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R1B	ENST00000254079.9	c.242-704C>T		intron_variant		1	NM_032192.4	P1

Frequencies

GnomAD3 genomes AF: 0.0183 AC: 2787 AN: 152118 Hom.: 207 Cov.: 32

Gnomad AFR AF: 0.00473

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0941

Gnomad ASJ AF: 0.00403

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.00850

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000691

Gnomad OTH AF: 0.0115

GnomAD4 exome AF: 0.0128 AC: 17 AN: 1324 Hom.: 3 Cov.: 0 AF XY: 0.00880 AC XY: 6 AN XY: 682

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0714

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.203

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0183 AC: 2779 AN: 152236 Hom.: 206 Cov.: 32 AF XY: 0.0218 AC XY: 1626 AN XY: 74432

Gnomad4 AFR AF: 0.00472

Gnomad4 AMR AF: 0.0937

Gnomad4 ASJ AF: 0.00403

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.00892

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000691

Gnomad4 OTH AF: 0.0113

Alfa AF: 0.0205 Hom.: 65

Bravo AF: 0.0260

Asia WGS AF: 0.0700 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.12
Cadd	Benign	21
Dann	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs12601930; hg19: chr17-37789432;