chr7-95102242-G-C

Variant names:

• chr7-95102242-G-C
• rs961262
• NM_001166160.2:c.1396-9017G>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.1396-9017G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,958 control chromosomes in the GnomAD database, including 20,012 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 0.50 (20012 hom., cov: 32)
• Consequence: PPP1R9A NM_001166160.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 6 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]

PPP1R9A-AS1 (HGNC:40696): (PPP1R9A antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 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.1396-9017G>C		intron	N/A	NP_001159632.1
	PPP1R9A	NM_001166161.1		c.1396-9017G>C		intron	N/A	NP_001159633.1
	PPP1R9A	NM_001166162.1		c.1396-9017G>C		intron	N/A	NP_001159634.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R9A	ENST00000433360.6	TSL:1 MANE Select	c.1396-9017G>C		intron	N/A	ENSP00000405514.1
	PPP1R9A	ENST00000289495.7	TSL:1	c.1396-9017G>C		intron	N/A	ENSP00000289495.7
	PPP1R9A	ENST00000456331.6	TSL:1	c.1396-9017G>C		intron	N/A	ENSP00000402893.2

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75868 AN: 151840 Hom.: 19980 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.515

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.500 AC: 75950 AN: 151958 Hom.: 20012 Cov.: 32 AF XY: 0.491 AC XY: 36466 AN XY: 74256

African (AFR) AF: 0.637 AC: 26388 AN: 41438

American (AMR) AF: 0.442 AC: 6749 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1948 AN: 3470

East Asian (EAS) AF: 0.114 AC: 592 AN: 5184

South Asian (SAS) AF: 0.245 AC: 1183 AN: 4820

European-Finnish (FIN) AF: 0.435 AC: 4574 AN: 10514

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32642 AN: 67954

Other (OTH) AF: 0.516 AC: 1086 AN: 2106

Alfa AF: 0.501 Hom.: 2462

Bravo AF: 0.510

Asia WGS AF: 0.260 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.43
PhyloP100		-0.54
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: rs961262; hg19: chr7-94731554;