dbSNP rs17773605: PPP1R9A:c.*4923G>T (chr7-95295226-G-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001166160.2(PPP1R9A):c.*4923G>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 0.0689 in 152,606 control chromosomes in the GnomAD database, including 780 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 0.069 ( 780 hom., cov: 33)

Exomes 𝑓: 0.051 ( 0 hom. )

Consequence

PPP1R9A
NM_001166160.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.813

Publications

5 publications found

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 was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R9A	NM_001166160.2 link	c.*4923G>T		3_prime_UTR_variant	Exon 20 of 20	ENST00000433360.6	NP_001159632.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
PPP1R9A	ENST00000433360.6 link	c.*4923G>T	3_prime_UTR_variant	Exon 20 of 20	1	NM_001166160.2	ENSP00000405514.1
PPP1R9A	ENST00000456331.6 link	c.*4923G>T	3_prime_UTR_variant	Exon 17 of 17	1		ENSP00000402893.2
PPP1R9A	ENST00000340694.8 link	c.*4923G>T	3_prime_UTR_variant	Exon 16 of 16	5		ENSP00000344524.4
PPP1R9A	ENST00000433881.5 link	c.*4923G>T	3_prime_UTR_variant	Exon 16 of 16	5		ENSP00000398870.1

Frequencies

GnomAD3 genomes

AF:

0.0690

AC:

10497

AN:

152054

Hom.:

785

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0282

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0967

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.416

Gnomad SAS

AF:

0.165

Gnomad FIN

AF:

0.0311

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0582

Gnomad OTH

AF:

0.0936

GnomAD4 exome

AF:

0.0507

AC:

AN:

434

Hom.:

Cov.:

AF XY:

0.0573

AC XY:

AN XY:

262

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0516

AC:

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

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

GnomAD4 genome

AF:

0.0690

AC:

10495

AN:

152172

Hom.:

780

Cov.:

AF XY:

0.0724

AC XY:

5388

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.0282

AC:

1170

AN:

41504

American (AMR)

AF:

0.0966

AC:

1478

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.113

AC:

392

AN:

3472

East Asian (EAS)

AF:

0.416

AC:

2147

AN:

5164

South Asian (SAS)

AF:

0.165

AC:

797

AN:

4816

European-Finnish (FIN)

AF:

0.0311

AC:

329

AN:

10576

Middle Eastern (MID)

AF:

0.0748

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0582

AC:

3956

AN:

68020

Other (OTH)

AF:

0.0955

AC:

202

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

479

958

1437

1916

2395

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

264

396

528

660

<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:

0.0673

Hom.:

870

Bravo

AF:

0.0735

Asia WGS

AF:

0.267

AC:

926

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

0.81

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