7-95242412-A-G

Variant names:

• chr7-95242412-A-G
• rs2374983
• NM_001166160.2:c.2113-5061A>G

Variant summary

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

The NM_001166160.2(PPP1R9A):​c.2113-5061A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,010 control chromosomes in the GnomAD database, including 12,328 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 0.39 (12328 hom., cov: 32)
• Consequence: PPP1R9A NM_001166160.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.484 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.2113-5061A>G		intron	N/A	NP_001159632.1	Q9ULJ8-3
	PPP1R9A	NM_001166161.1		c.2047-5061A>G		intron	N/A	NP_001159633.1	Q9ULJ8-5
	PPP1R9A	NM_001166162.1		c.2047-5061A>G		intron	N/A	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.2113-5061A>G		intron	N/A	ENSP00000405514.1	Q9ULJ8-3
	PPP1R9A	ENST00000289495.7	TSL:1	c.2047-5061A>G		intron	N/A	ENSP00000289495.7	Q9ULJ8-5
	PPP1R9A	ENST00000456331.6	TSL:1	c.2047-5061A>G		intron	N/A	ENSP00000402893.2	Q9ULJ8-4

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59388 AN: 151892 Hom.: 12327 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.391 AC: 59406 AN: 152010 Hom.: 12328 Cov.: 32 AF XY: 0.393 AC XY: 29190 AN XY: 74308

African (AFR) AF: 0.248 AC: 10263 AN: 41462

American (AMR) AF: 0.384 AC: 5865 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1896 AN: 5156

South Asian (SAS) AF: 0.501 AC: 2413 AN: 4820

European-Finnish (FIN) AF: 0.481 AC: 5090 AN: 10572

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31536 AN: 67958

Other (OTH) AF: 0.358 AC: 755 AN: 2108

Alfa AF: 0.435 Hom.: 62620

Bravo AF: 0.372

Asia WGS AF: 0.399 AC: 1383 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.36
PhyloP100		0.69
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: rs2374983; hg19: chr7-94871724;