rs1495099

Variant names:

• chr17-39628211-C-G
• rs1495099
• NM_032192.4:c.81+738C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 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]

ENSG00000306125 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PPP1R1B	NM_032192.4	c.81+738C>G		intron_variant	Intron 1 of 6	ENST00000254079.9	NP_115568.2
PPP1R1B	XM_017025216.3	c.81+738C>G		intron_variant	Intron 2 of 7		XP_016880705.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R1B	ENST00000254079.9	c.81+738C>G		intron_variant	Intron 1 of 6	1	NM_032192.4	ENSP00000254079.4

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

African (AFR) AF: 0.231 AC: 9496 AN: 41114

American (AMR) AF: 0.551 AC: 8380 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2325 AN: 3466

East Asian (EAS) AF: 0.442 AC: 2245 AN: 5084

South Asian (SAS) AF: 0.708 AC: 3367 AN: 4754

European-Finnish (FIN) AF: 0.730 AC: 7639 AN: 10458

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47459 AN: 67720

Other (OTH) AF: 0.567 AC: 1189 AN: 2096

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
PhyloP100		0.0090
PromoterAI		-0.0063	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1495099; hg19: chr17-37784464;