Genetic Variant 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021959.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R11	NM_021959.3	MANE Select	c.*603T>C		3_prime_UTR	Exon 3 of 3	NP_068778.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PPP1R11	ENST00000376772.8	TSL:1 MANE Select	c.*603T>C	3_prime_UTR	Exon 3 of 3	ENSP00000365963.3
PPP1R11	ENST00000376758.1	TSL:2	c.*603T>C	3_prime_UTR	Exon 2 of 2	ENSP00000365949.1
PPP1R11	ENST00000376763.5	TSL:3	c.*603T>C	3_prime_UTR	Exon 4 of 4	ENSP00000365954.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over