8-9139905-G-A

Position:

• chr8-9139905-G-A

Variant summary

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

The NM_024607.4(PPP1R3B):​c.*889C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,024 control chromosomes in the GnomAD database, including 7,667 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 0.29 (7666 hom., cov: 32)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: PPP1R3B NM_024607.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14

Genes affected

PPP1R3B (HGNC:14942): (protein phosphatase 1 regulatory subunit 3B) This gene encodes the catalytic subunit of the serine/theonine phosphatase, protein phosphatase-1. The encoded protein is expressed in liver and skeletal muscle tissue and may be involved in regulating glycogen synthesis in these tissues. This gene may be a involved in type 2 diabetes and maturity-onset diabetes of the young. Alternate splicing results in multiple transcript variants that encode the same protein.[provided by RefSeq, Jan 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP1R3B	NM_024607.4	c.*889C>T		3_prime_UTR_variant	2/2	ENST00000310455.4	NP_078883.2
PPP1R3B	NM_001201329.2	c.*889C>T		3_prime_UTR_variant	2/2		NP_001188258.1
PPP1R3B	XM_006716253.4	c.*889C>T		3_prime_UTR_variant	2/2		XP_006716316.1
PPP1R3B	XM_047422235.1	c.*889C>T		3_prime_UTR_variant	2/2		XP_047278191.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R3B	ENST00000310455	c.*889C>T		3_prime_UTR_variant	2/2	1	NM_024607.4	ENSP00000308318.3
PPP1R3B	ENST00000519699	c.*889C>T		3_prime_UTR_variant	2/2	2		ENSP00000428642.1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44186 AN: 151888 Hom.: 7672 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.325

GnomAD4 exome AF: 0.167 AC: 3 AN: 18 Hom.: 1 Cov.: 0 AF XY: 0.0714 AC XY: 1 AN XY: 14

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.125

GnomAD4 genome AF: 0.291 AC: 44204 AN: 152006 Hom.: 7666 Cov.: 32 AF XY: 0.298 AC XY: 22137 AN XY: 74286

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.326

Alfa AF: 0.310 Hom.: 7402

Bravo AF: 0.298

Asia WGS AF: 0.557 AC: 1932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	9.8
DANN	Benign	0.79

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

Publications

LitVar

Other links and lift over

dbSNP: rs330919; hg19: chr8-8997415;