chr7-95294544-G-A

Variant names:

• chr7-95294544-G-A
• rs854547
• NM_001166160.2:c.*4241G>A

Variant summary

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

The NM_001166160.2(PPP1R9A):​c.*4241G>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 0.54 in 151,978 control chromosomes in the GnomAD database, including 23,119 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 0.54 (23115 hom., cov: 31)
  • Exomes 𝑓: 0.90 (4 hom.)
• Consequence: PPP1R9A NM_001166160.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635
• Publications: 23 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 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.*4241G>A		3_prime_UTR	Exon 20 of 20	NP_001159632.1	Q9ULJ8-3
	PPP1R9A	NM_001166161.1		c.*4241G>A		3_prime_UTR	Exon 18 of 18	NP_001159633.1	Q9ULJ8-5
	PPP1R9A	NM_001166162.1		c.*4241G>A		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.*4241G>A		3_prime_UTR	Exon 20 of 20	ENSP00000405514.1	Q9ULJ8-3
	PPP1R9A	ENST00000456331.6	TSL:1	c.*4241G>A		3_prime_UTR	Exon 17 of 17	ENSP00000402893.2	Q9ULJ8-4
	PPP1R9A	ENST00000969570.1		c.*4241G>A		3_prime_UTR	Exon 21 of 21	ENSP00000639629.1

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81978 AN: 151850 Hom.: 23116 Cov.: 31

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.573

GnomAD4 exome AF: 0.900 AC: 9 AN: 10 Hom.: 4 Cov.: 0 AF XY: 1.00 AC XY: 8 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

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: 0.833 AC: 5 AN: 6

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.540 AC: 81988 AN: 151968 Hom.: 23115 Cov.: 31 AF XY: 0.538 AC XY: 39981 AN XY: 74256

African (AFR) AF: 0.374 AC: 15495 AN: 41438

American (AMR) AF: 0.564 AC: 8598 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2067 AN: 3472

East Asian (EAS) AF: 0.359 AC: 1856 AN: 5170

South Asian (SAS) AF: 0.602 AC: 2901 AN: 4818

European-Finnish (FIN) AF: 0.577 AC: 6071 AN: 10528

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.633 AC: 43022 AN: 67972

Other (OTH) AF: 0.567 AC: 1198 AN: 2112

Alfa AF: 0.597 Hom.: 83346

Bravo AF: 0.528

Asia WGS AF: 0.449 AC: 1564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.71
PhyloP100		0.64
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: rs854547; hg19: chr7-94923856;