rs907094

Variant names:

• chr17-39634118-G-A
• rs907094
• NM_032192.4:c.445+32G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-39634118-G-A
• chr17-39634118-G-C
• chr17-39634118-G-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+32G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 1,611,418 control chromosomes in the GnomAD database, including 452,561 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 (31345 hom., cov: 32)
  • Exomes 𝑓: 0.75 (421216 hom.)
• Consequence: PPP1R1B NM_032192.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 64 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R1B	NM_032192.4	MANE Select	c.445+32G>A		intron	N/A	NP_115568.2
	PPP1R1B	NM_001242464.2		c.337+32G>A		intron	N/A	NP_001229393.1	Q9UD71-2
	PPP1R1B	NM_181505.4		c.337+32G>A		intron	N/A	NP_852606.1	Q9UD71-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R1B	ENST00000254079.9	TSL:1 MANE Select	c.445+32G>A		intron	N/A	ENSP00000254079.4	Q9UD71-1
	PPP1R1B	ENST00000394265.5	TSL:1	c.337+32G>A		intron	N/A	ENSP00000377808.1	Q9UD71-2
	PPP1R1B	ENST00000394267.2	TSL:1	c.337+32G>A		intron	N/A	ENSP00000377810.2	Q9UD71-2

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91624 AN: 151974 Hom.: 31340 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.634

GnomAD2 exomes AF: 0.694 AC: 173419 AN: 249982 AF XY: 0.711

Gnomad AFR exome AF: 0.260

Gnomad AMR exome AF: 0.640

Gnomad ASJ exome AF: 0.746

Gnomad EAS exome AF: 0.415

Gnomad FIN exome AF: 0.784

Gnomad NFE exome AF: 0.779

Gnomad OTH exome AF: 0.731

GnomAD4 exome AF: 0.753 AC: 1099022 AN: 1459326 Hom.: 421216 Cov.: 41 AF XY: 0.755 AC XY: 547981 AN XY: 725876

African (AFR) AF: 0.261 AC: 8717 AN: 33426

American (AMR) AF: 0.636 AC: 28433 AN: 44698

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 19355 AN: 26120

East Asian (EAS) AF: 0.481 AC: 19095 AN: 39680

South Asian (SAS) AF: 0.758 AC: 65277 AN: 86146

European-Finnish (FIN) AF: 0.780 AC: 41242 AN: 52844

Middle Eastern (MID) AF: 0.766 AC: 3913 AN: 5110

European-Non Finnish (NFE) AF: 0.783 AC: 869567 AN: 1111036

Other (OTH) AF: 0.721 AC: 43423 AN: 60266

GnomAD4 genome AF: 0.603 AC: 91647 AN: 152092 Hom.: 31345 Cov.: 32 AF XY: 0.602 AC XY: 44765 AN XY: 74378

African (AFR) AF: 0.272 AC: 11284 AN: 41486

American (AMR) AF: 0.612 AC: 9347 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2560 AN: 3468

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

South Asian (SAS) AF: 0.723 AC: 3487 AN: 4822

European-Finnish (FIN) AF: 0.778 AC: 8239 AN: 10594

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

European-Non Finnish (NFE) AF: 0.768 AC: 52208 AN: 67962

Other (OTH) AF: 0.634 AC: 1337 AN: 2110

Alfa AF: 0.711 Hom.: 112626

Bravo AF: 0.575

Asia WGS AF: 0.610 AC: 2123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.67
PhyloP100		-1.8
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: rs907094; hg19: chr17-37790371; COSMIC: COSV54203141; COSMIC: COSV54203141;