17-39634686-C-T

Variant names:

• chr17-39634686-C-T
• rs3764352
• NM_032192.4:c.445+600C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032192.4(PPP1R1B):​c.445+600C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,166 control chromosomes in the GnomAD database, including 31,377 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 (31377 hom., cov: 33)
• Consequence: PPP1R1B NM_032192.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 35 publications found

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]

ENSG00000306162 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R1B	NM_032192.4	MANE Select	c.445+600C>T		intron	N/A	NP_115568.2
	PPP1R1B	NM_001242464.2		c.337+600C>T		intron	N/A	NP_001229393.1
	PPP1R1B	NM_181505.4		c.337+600C>T		intron	N/A	NP_852606.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R1B	ENST00000254079.9	TSL:1 MANE Select	c.445+600C>T		intron	N/A	ENSP00000254079.4
	PPP1R1B	ENST00000394265.5	TSL:1	c.337+600C>T		intron	N/A	ENSP00000377808.1
	PPP1R1B	ENST00000394267.2	TSL:1	c.337+600C>T		intron	N/A	ENSP00000377810.2

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91701 AN: 152048 Hom.: 31372 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.634

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.603 AC: 91724 AN: 152166 Hom.: 31377 Cov.: 33 AF XY: 0.602 AC XY: 44791 AN XY: 74396

African (AFR) AF: 0.272 AC: 11285 AN: 41490

American (AMR) AF: 0.612 AC: 9354 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2564 AN: 3472

East Asian (EAS) AF: 0.444 AC: 2293 AN: 5166

South Asian (SAS) AF: 0.723 AC: 3494 AN: 4830

European-Finnish (FIN) AF: 0.778 AC: 8247 AN: 10602

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52257 AN: 67994

Other (OTH) AF: 0.634 AC: 1340 AN: 2114

Alfa AF: 0.712 Hom.: 50523

Bravo AF: 0.575

Asia WGS AF: 0.612 AC: 2130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.74
DANN	Benign	0.54
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3764352; hg19: chr17-37790939;