rs330915

Variant names:

• chr8-9139426-T-A
• rs330915
• NM_024607.4:c.*1368A>T

Your query was ambiguous. Multiple possible variants found:

• chr8-9139426-T-A
• chr8-9139426-T-C

Variant summary

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

The NM_024607.4(PPP1R3B):​c.*1368A>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 0.299 in 152,148 control chromosomes in the GnomAD database, including 7,948 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.30 (7948 hom., cov: 33)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: PPP1R3B NM_024607.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535
• Publications: 6 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024607.4. 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
	PPP1R3B	NM_024607.4	MANE Select	c.*1368A>T		3_prime_UTR	Exon 2 of 2	NP_078883.2
	PPP1R3B	NM_001201329.2		c.*1368A>T		3_prime_UTR	Exon 2 of 2	NP_001188258.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R3B	ENST00000310455.4	TSL:1 MANE Select	c.*1368A>T		3_prime_UTR	Exon 2 of 2	ENSP00000308318.3
	PPP1R3B	ENST00000519699.1	TSL:2	c.*1368A>T		downstream_gene	N/A	ENSP00000428642.1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45537 AN: 152022 Hom.: 7951 Cov.: 33

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.332

GnomAD4 exome AF: 0.125 AC: 1 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.299 AC: 45563 AN: 152140 Hom.: 7948 Cov.: 33 AF XY: 0.306 AC XY: 22755 AN XY: 74380

African (AFR) AF: 0.196 AC: 8142 AN: 41496

American (AMR) AF: 0.399 AC: 6108 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3470

East Asian (EAS) AF: 0.754 AC: 3902 AN: 5174

South Asian (SAS) AF: 0.535 AC: 2580 AN: 4826

European-Finnish (FIN) AF: 0.246 AC: 2606 AN: 10594

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20125 AN: 67980

Other (OTH) AF: 0.333 AC: 701 AN: 2106

Alfa AF: 0.272 Hom.: 769

Bravo AF: 0.308

Asia WGS AF: 0.557 AC: 1931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.71
PhyloP100		-0.54
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: rs330915; hg19: chr8-8996936;