rs1495099

chr17-39628211-C-G

Variant summary

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

The NM_032192.4(PPP1R1B):c.81+738C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,104 control chromosomes in the GnomAD database, including 26,097 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 0.55 (26097 hom., cov: 27)
• Consequence: PPP1R1B NM_032192.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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=-0.57).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP1R1B	NM_032192.4	c.81+738C>G		intron_variant		ENST00000254079.9
PPP1R1B	XM_017025216.3	c.81+738C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R1B	ENST00000254079.9	c.81+738C>G		intron_variant		1	NM_032192.4	P1
PPP1R1B	ENST00000579000.5	c.81+738C>G		intron_variant		5
PPP1R1B	ENST00000580825.5	c.81+738C>G		intron_variant		5		P1
PPP1R1B	ENST00000582680.5	c.72+747C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.549 AC: 82911 AN: 150988 Hom.: 26089 Cov.: 27

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.549 AC: 82931 AN: 151104 Hom.: 26097 Cov.: 27 AF XY: 0.548 AC XY: 40453 AN XY: 73754

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.567

Alfa AF: 0.596 Hom.: 3241

Bravo AF: 0.520

Asia WGS AF: 0.602 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	13
Dann	Benign	0.88

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: rs1495099; hg19: chr17-37784464;