7-95291168-T-C

Variant names:

• chr7-95291168-T-C
• rs854541
• NM_001166160.2:c.*865T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001166160.2(PPP1R9A):​c.*865T>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 0.557 in 151,952 control chromosomes in the GnomAD database, including 24,112 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 0.56 (24112 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: PPP1R9A NM_001166160.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166160.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R9A	NM_001166160.2	MANE Select	c.*865T>C		3_prime_UTR	Exon 20 of 20	NP_001159632.1	Q9ULJ8-3
	PPP1R9A	NM_001166161.1		c.*865T>C		3_prime_UTR	Exon 18 of 18	NP_001159633.1	Q9ULJ8-5
	PPP1R9A	NM_001166162.1		c.*865T>C		3_prime_UTR	Exon 17 of 17	NP_001159634.1	Q9ULJ8-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R9A	ENST00000433360.6	TSL:1 MANE Select	c.*865T>C		3_prime_UTR	Exon 20 of 20	ENSP00000405514.1	Q9ULJ8-3
	PPP1R9A	ENST00000456331.6	TSL:1	c.*865T>C		3_prime_UTR	Exon 17 of 17	ENSP00000402893.2	Q9ULJ8-4
	PPP1R9A	ENST00000969576.1		c.*865T>C		3_prime_UTR	Exon 19 of 19	ENSP00000639635.1

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84522 AN: 151826 Hom.: 24070 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.598

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 3 AN: 6

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.557 AC: 84624 AN: 151944 Hom.: 24112 Cov.: 31 AF XY: 0.554 AC XY: 41124 AN XY: 74238

African (AFR) AF: 0.668 AC: 27690 AN: 41422

American (AMR) AF: 0.569 AC: 8682 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2306 AN: 3472

East Asian (EAS) AF: 0.586 AC: 3024 AN: 5158

South Asian (SAS) AF: 0.444 AC: 2136 AN: 4806

European-Finnish (FIN) AF: 0.440 AC: 4639 AN: 10550

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34345 AN: 67958

Other (OTH) AF: 0.595 AC: 1254 AN: 2108

Alfa AF: 0.531 Hom.: 66353

Bravo AF: 0.578

Asia WGS AF: 0.508 AC: 1772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.46
DANN	Benign	0.74
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs854541; hg19: chr7-94920480;