dbSNP rs1884056: PPP1R3E:c.*1922C>T (chr14-23297382-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001276318.2(PPP1R3E):c.*1922C>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 0.265 in 152,152 control chromosomes in the GnomAD database, including 6,323 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 0.26 ( 6318 hom., cov: 32)

Exomes 𝑓: 0.35 ( 5 hom. )

Consequence

PPP1R3E
NM_001276318.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.252

Publications

14 publications found

Variant links:

Genes affected

PPP1R3E (HGNC:14943): (protein phosphatase 1 regulatory subunit 3E) Predicted to enable [phosphorylase] phosphatase activity; glycogen binding activity; and protein phosphatase 1 binding activity. Predicted to be involved in positive regulation of glycogen biosynthetic process. Predicted to be located in glycogen granule. Predicted to be part of protein phosphatase type 1 complex. [provided by Alliance of Genome Resources, Apr 2022]

PPP1R3E links:

HOMEZ (HGNC:20164): (homeobox and leucine zipper encoding) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in cytosol; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

HOMEZ links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R3E	NM_001276318.2 link	c.*1922C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000452015.9	NP_001263247.1	Q9H7J1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PPP1R3E	ENST00000452015.9 link	c.*1922C>T	3_prime_UTR_variant	Exon 5 of 5	2	NM_001276318.2	ENSP00000408288.3	Q9H7J1
PPP1R3E	ENST00000558058.5 link	c.*1727C>T	3_prime_UTR_variant	Exon 4 of 4	3		ENSP00000453175.1	H0YLE3
PPP1R3E	ENST00000559314.5 link	c.*1242C>T	3_prime_UTR_variant	Exon 5 of 5	2		ENSP00000454106.1	H0YNQ2
HOMEZ	ENST00000561013.3 link	c.-113+2019C>T	intron_variant	Intron 1 of 2	2		ENSP00000453979.1	Q8IX15-3

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40283

AN:

151974

Hom.:

6321

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0927

Gnomad AMI

AF:

0.619

Gnomad AMR

AF:

0.325

Gnomad ASJ

AF:

0.348

Gnomad EAS

AF:

0.494

Gnomad SAS

AF:

0.276

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.317

Gnomad OTH

AF:

0.269

GnomAD4 exome

AF:

0.350

AC:

AN:

Hom.:

Cov.:

AF XY:

0.396

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.348

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.265

AC:

40283

AN:

152092

Hom.:

6318

Cov.:

AF XY:

0.270

AC XY:

20100

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.0925

AC:

3839

AN:

41514

American (AMR)

AF:

0.326

AC:

4970

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.348

AC:

1207

AN:

3468

East Asian (EAS)

AF:

0.495

AC:

2554

AN:

5164

South Asian (SAS)

AF:

0.277

AC:

1335

AN:

4822

European-Finnish (FIN)

AF:

0.343

AC:

3626

AN:

10584

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.317

AC:

21534

AN:

67962

Other (OTH)

AF:

0.266

AC:

561

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1433

2866

4300

5733

7166

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

422

844

1266

1688

2110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.304

Hom.:

33336

Bravo

AF:

0.261

Asia WGS

AF:

0.299

AC:

1041

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.7

(source)

DANN

Benign

0.54

PhyloP100

0.25

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over