rs17773605

chr7-95295226-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.813

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PPP1R9A	NM_001166160.2	c.*4923G>T		3_prime_UTR_variant	20/20	ENST00000433360.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R9A	ENST00000433360.6	c.*4923G>T		3_prime_UTR_variant	20/20	1	NM_001166160.2
PPP1R9A	ENST00000456331.6	c.*4923G>T		3_prime_UTR_variant	17/17	1
PPP1R9A	ENST00000340694.8	c.*4923G>T		3_prime_UTR_variant	16/16	5		A1
PPP1R9A	ENST00000433881.5	c.*4923G>T		3_prime_UTR_variant	16/16	5		A1

Frequencies

GnomAD3 genomes AF: 0.0690 AC: 10497 AN: 152054 Hom.: 785 Cov.: 33

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: 22 AN: 434 Hom.: 0 Cov.: 0 AF XY: 0.0573 AC XY: 15 AN XY: 262

Gnomad4 FIN exome AF: 0.0516

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0690 AC: 10495 AN: 152172 Hom.: 780 Cov.: 33 AF XY: 0.0724 AC XY: 5388 AN XY: 74378

Gnomad4 AFR AF: 0.0282

Gnomad4 AMR AF: 0.0966

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0311

Gnomad4 NFE AF: 0.0582

Gnomad4 OTH AF: 0.0955

Alfa AF: 0.0702 Hom.: 695

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	11
Dann	Benign	0.76

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

Other links and lift over

dbSNP: rs17773605; hg19: chr7-94924538; COSMIC: COSV55931652; COSMIC: COSV55931652;