dbSNP rs8347: PPP1R11:c.*603T>C (chr6-30069909-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_021959.3(PPP1R11):c.*603T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,240 control chromosomes in the GnomAD database, including 6,029 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 0.24 ( 6029 hom., cov: 31)

Exomes 𝑓: 0.095 ( 0 hom. )

Consequence

PPP1R11
NM_021959.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.870

Publications

8 publications found

Variant links:

Genes affected

PPP1R11 (HGNC:9285): (protein phosphatase 1 regulatory inhibitor subunit 11) This gene encodes a specific inhibitor of protein phosphatase-1 (PP1) with a differential sensitivity toward the metal-independent and metal-dependent forms of PP1. The gene is located within the major histocompatibility complex class I region on chromosome 6. [provided by RefSeq, Jul 2008]

PPP1R11 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PPP1R11	NM_021959.3 link	c.*603T>C	3_prime_UTR_variant	Exon 3 of 3	ENST00000376772.8	NP_068778.1	O60927A2BEK1
PPP1R11	XM_047419279.1 link	c.*603T>C	3_prime_UTR_variant	Exon 4 of 4		XP_047275235.1
PPP1R11	XM_047419280.1 link	c.*603T>C	3_prime_UTR_variant	Exon 5 of 5		XP_047275236.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R11	ENST00000376772.8 link	c.*603T>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_021959.3	ENSP00000365963.3		O60927

Frequencies

GnomAD3 genomes

AF:

0.241

AC:

36593

AN:

151964

Hom.:

6010

Cov.:

show subpopulations

Gnomad AFR

AF:

0.455

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.266

Gnomad ASJ

AF:

0.346

Gnomad EAS

AF:

0.191

Gnomad SAS

AF:

0.192

Gnomad FIN

AF:

0.0504

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.275

GnomAD4 exome

AF:

0.0949

AC:

AN:

158

Hom.:

Cov.:

AF XY:

0.100

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0732

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.241

AC:

36651

AN:

152082

Hom.:

6029

Cov.:

AF XY:

0.236

AC XY:

17521

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.454

AC:

18826

AN:

41428

American (AMR)

AF:

0.266

AC:

4064

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.346

AC:

1202

AN:

3470

East Asian (EAS)

AF:

0.192

AC:

992

AN:

5174

South Asian (SAS)

AF:

0.193

AC:

931

AN:

4818

European-Finnish (FIN)

AF:

0.0504

AC:

535

AN:

10614

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.139

AC:

9419

AN:

67982

Other (OTH)

AF:

0.273

AC:

574

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1246

2492

3739

4985

6231

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

354

708

1062

1416

1770

<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:

0.188

Hom.:

741

Bravo

AF:

0.272

Asia WGS

AF:

0.228

AC:

794

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.99

(source)

DANN

Benign

0.53

PhyloP100

-0.87

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over