rs10485996

Variant names:

• chr7-95093473-C-A
• rs10485996
• NM_001166160.2:c.1396-17786C>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.1396-17786C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,146 control chromosomes in the GnomAD database, including 1,577 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 0.12 (1577 hom., cov: 32)
• Consequence: PPP1R9A NM_001166160.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 5 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 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.1396-17786C>A		intron	N/A	NP_001159632.1
	PPP1R9A	NM_001166161.1		c.1396-17786C>A		intron	N/A	NP_001159633.1
	PPP1R9A	NM_001166162.1		c.1396-17786C>A		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.1396-17786C>A		intron	N/A	ENSP00000405514.1
	PPP1R9A	ENST00000289495.7	TSL:1	c.1396-17786C>A		intron	N/A	ENSP00000289495.7
	PPP1R9A	ENST00000456331.6	TSL:1	c.1396-17786C>A		intron	N/A	ENSP00000402893.2

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18922 AN: 152028 Hom.: 1581 Cov.: 32

Gnomad AFR AF: 0.0326

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.124 AC: 18914 AN: 152146 Hom.: 1577 Cov.: 32 AF XY: 0.123 AC XY: 9141 AN XY: 74382

African (AFR) AF: 0.0325 AC: 1350 AN: 41518

American (AMR) AF: 0.145 AC: 2213 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1531 AN: 5176

South Asian (SAS) AF: 0.117 AC: 562 AN: 4818

European-Finnish (FIN) AF: 0.0975 AC: 1033 AN: 10594

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11360 AN: 67980

Other (OTH) AF: 0.129 AC: 272 AN: 2106

Alfa AF: 0.156 Hom.: 3516

Bravo AF: 0.126

Asia WGS AF: 0.192 AC: 666 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	15
DANN	Benign	0.64
PhyloP100		0.53
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: rs10485996; hg19: chr7-94722785;