Variant 7-94910228-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001166160.2(PPP1R9A):c.115T>A(p.Ser39Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00568 in 1,613,640 control chromosomes in the GnomAD database, including 475 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.030 ( 248 hom., cov: 32)

Exomes 𝑓: 0.0031 ( 227 hom. )

Consequence

PPP1R9A
NM_001166160.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.964

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0014253259).

BP6

Variant 7-94910228-T-A is Benign according to our data. Variant chr7-94910228-T-A is described in ClinVar as [Benign]. Clinvar id is 776241.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 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.115T>A	p.Ser39Thr	missense_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.115T>A	p.Ser39Thr	missense_variant	2/20	1	NM_001166160.2		Q9ULJ8-3

Frequencies

GnomAD3 genomes

AF:

0.0303

AC:

4594

AN:

151704

Hom.:

246

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00945

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000368

Gnomad OTH

AF:

0.0212

GnomAD3 exomes

AF:

0.00809

AC:

2032

AN:

251294

Hom.:

AF XY:

0.00576

AC XY:

782

AN XY:

135826

show subpopulations

Gnomad AFR exome

AF:

0.110

Gnomad AMR exome

AF:

0.00535

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000163

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000334

Gnomad OTH exome

AF:

0.00342

GnomAD4 exome

AF:

0.00312

AC:

4563

AN:

1461820

Hom.:

227

Cov.:

AF XY:

0.00265

AC XY:

1930

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.110

Gnomad4 AMR exome

AF:

0.00608

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000104

Gnomad4 FIN exome

AF:

0.0000375

Gnomad4 NFE exome

AF:

0.000181

Gnomad4 OTH exome

AF:

0.00652

GnomAD4 genome

AF:

0.0303

AC:

4602

AN:

151820

Hom.:

248

Cov.:

AF XY:

0.0284

AC XY:

2107

AN XY:

74184

show subpopulations

Gnomad4 AFR

AF:

0.106

Gnomad4 AMR

AF:

0.00943

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000368

Gnomad4 OTH

AF:

0.0210

Alfa

AF:

0.00462

Hom.:

Bravo

AF:

0.0342

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.000519

AC:

ESP6500AA

AF:

0.101

AC:

444

ESP6500EA

AF:

0.000349

AC:

ExAC

AF:

0.00988

AC:

1199

Asia WGS

AF:

0.00866

AC:

AN:

3478

EpiCase

AF:

0.000327

EpiControl

AF:

0.000415

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Nov 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.063

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.57

Cadd

Benign

Dann

Benign

0.92

DEOGEN2

Benign

0.023

T;.;T;.;T;T;.;.

Eigen

Benign

0.025

Eigen_PC

Benign

0.053

FATHMM_MKL

Benign

0.76

LIST_S2

Benign

0.82

T;T;T;.;T;.;T;T

MetaRNN

Benign

0.0014

T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

0.97

N;N;N;N;N;N

PrimateAI

Benign

0.48

PROVEAN

Benign

-1.2

N;N;N;N;N;N;N;N

REVEL

Benign

0.033

Sift

Benign

0.28

T;D;D;D;T;D;D;D

Sift4G

Benign

0.37

T;T;T;T;T;T;T;T

Polyphen

0.36

.;.;B;.;.;B;.;.

Vest4

0.33, 0.25, 0.33, 0.25, 0.22, 0.34

MVP

0.44

MPC

0.22

ClinPred

0.0099

GERP RS

1.7

Varity_R

0.084

gMVP

0.11

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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