Variant 7-94910224-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_001166160.2(PPP1R9A):c.111C>T(p.Pro37=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 1,613,752 control chromosomes in the GnomAD database, including 7,951 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.082 ( 639 hom., cov: 32)

Exomes 𝑓: 0.095 ( 7312 hom. )

Consequence

PPP1R9A
NM_001166160.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.140

Variant links:

Genes affected

PPP1R9A (HGNC:14946): (protein phosphatase 1 regulatory subunit 9A) This gene is imprinted, and located in a cluster of imprinted genes on chromosome 7q12. This gene is transcribed in both neuronal and multiple embryonic tissues, and it is maternally expressed mainly in embryonic skeletal muscle tissues and biallelically expressed in other embryonic tissues. The protein encoded by this gene includes a PDZ domain and a sterile alpha motif (SAM). It is a regulatory subunit of protein phosphatase I, and controls actin cytoskeleton reorganization. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]

PPP1R9A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 7-94910224-C-T is Benign according to our data. Variant chr7-94910224-C-T is described in ClinVar as [Benign]. Clinvar id is 3060118.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.14 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP1R9A	NM_001166160.2 linkuse as main transcript	c.111C>T	p.Pro37=	synonymous_variant	2/20	ENST00000433360.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R9A	ENST00000433360.6 linkuse as main transcript	c.111C>T	p.Pro37=	synonymous_variant	2/20	1	NM_001166160.2		Q9ULJ8-3

Frequencies

GnomAD3 genomes

AF:

0.0825

AC:

12534

AN:

151950

Hom.:

635

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0311

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.154

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.0845

Gnomad OTH

AF:

0.101

GnomAD3 exomes

AF:

0.112

AC:

28046

AN:

251152

Hom.:

1915

AF XY:

0.109

AC XY:

14827

AN XY:

135758

show subpopulations

Gnomad AFR exome

AF:

0.0298

Gnomad AMR exome

AF:

0.223

Gnomad ASJ exome

AF:

0.106

Gnomad EAS exome

AF:

0.132

Gnomad SAS exome

AF:

0.117

Gnomad FIN exome

AF:

0.103

Gnomad NFE exome

AF:

0.0872

Gnomad OTH exome

AF:

0.106

GnomAD4 exome

AF:

0.0947

AC:

138369

AN:

1461684

Hom.:

7312

Cov.:

AF XY:

0.0950

AC XY:

69074

AN XY:

727130

show subpopulations

Gnomad4 AFR exome

AF:

0.0306

Gnomad4 AMR exome

AF:

0.219

Gnomad4 ASJ exome

AF:

0.110

Gnomad4 EAS exome

AF:

0.150

Gnomad4 SAS exome

AF:

0.121

Gnomad4 FIN exome

AF:

0.103

Gnomad4 NFE exome

AF:

0.0864

Gnomad4 OTH exome

AF:

0.102

GnomAD4 genome

AF:

0.0825

AC:

12544

AN:

152068

Hom.:

639

Cov.:

AF XY:

0.0851

AC XY:

6324

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.0311

Gnomad4 AMR

AF:

0.155

Gnomad4 ASJ

AF:

0.117

Gnomad4 EAS

AF:

0.141

Gnomad4 SAS

AF:

0.124

Gnomad4 FIN

AF:

0.102

Gnomad4 NFE

AF:

0.0845

Gnomad4 OTH

AF:

0.101

Alfa

AF:

0.0852

Hom.:

1115

Bravo

AF:

0.0847

Asia WGS

AF:

0.122

AC:

425

AN:

3478

EpiCase

AF:

0.0896

EpiControl

AF:

0.0875

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

PPP1R9A-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 28, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

Cadd

Benign

Dann

Benign

0.62

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over