rs854543

Variant names:

• chr7-95292231-C-A
• rs854543
• NM_001166160.2:c.*1928C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-95292231-C-A
• chr7-95292231-C-G
• chr7-95292231-C-T

Variant summary

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

The NM_001166160.2(PPP1R9A):​c.*1928C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,426 control chromosomes in the GnomAD database, including 49,410 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 0.80 (49335 hom., cov: 33)
  • Exomes 𝑓: 0.73 (75 hom.)
• Consequence: PPP1R9A NM_001166160.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R9A	NM_001166160.2	MANE Select	c.*1928C>A		3_prime_UTR	Exon 20 of 20	NP_001159632.1
	PPP1R9A	NM_001166161.1		c.*1928C>A		3_prime_UTR	Exon 18 of 18	NP_001159633.1
	PPP1R9A	NM_001166162.1		c.*1928C>A		3_prime_UTR	Exon 17 of 17	NP_001159634.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R9A	ENST00000433360.6	TSL:1 MANE Select	c.*1928C>A		3_prime_UTR	Exon 20 of 20	ENSP00000405514.1
	PPP1R9A	ENST00000456331.6	TSL:1	c.*1928C>A		3_prime_UTR	Exon 17 of 17	ENSP00000402893.2
	PPP1R9A	ENST00000340694.8	TSL:5	c.*1928C>A		3_prime_UTR	Exon 16 of 16	ENSP00000344524.4

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122277 AN: 152022 Hom.: 49294 Cov.: 33

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.830

GnomAD4 exome AF: 0.734 AC: 210 AN: 286 Hom.: 75 Cov.: 0 AF XY: 0.722 AC XY: 130 AN XY: 180

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) AF: 0.730 AC: 206 AN: 282

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.804 AC: 122375 AN: 152140 Hom.: 49335 Cov.: 33 AF XY: 0.806 AC XY: 59949 AN XY: 74354

African (AFR) AF: 0.805 AC: 33394 AN: 41506

American (AMR) AF: 0.858 AC: 13117 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2950 AN: 3468

East Asian (EAS) AF: 0.893 AC: 4631 AN: 5184

South Asian (SAS) AF: 0.862 AC: 4164 AN: 4830

European-Finnish (FIN) AF: 0.729 AC: 7690 AN: 10544

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53776 AN: 67998

Other (OTH) AF: 0.825 AC: 1746 AN: 2116

Alfa AF: 0.799 Hom.: 66822

Bravo AF: 0.815

Asia WGS AF: 0.842 AC: 2931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.33
PhyloP100		0.76
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: rs854543; hg19: chr7-94921543;