rs3789911

Variant names:

• chr9-135480891-G-A
• rs3789911
• NM_014811.5:c.-329+869G>A

Variant summary

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

The NM_014811.5(PPP1R26):​c.-329+869G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,402 control chromosomes in the GnomAD database, including 49,644 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 (49575 hom., cov: 33)
  • Exomes 𝑓: 0.76 (69 hom.)
• Consequence: PPP1R26 NM_014811.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• Publications: 5 publications found

Genes affected

PPP1R26 (HGNC:29089): (protein phosphatase 1 regulatory subunit 26) Predicted to enable protein phosphatase inhibitor activity. Predicted to be involved in negative regulation of phosphatase activity. Predicted to be located in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

PPP1R26-AS1 (HGNC:48717): (PPP1R26 antisense RNA 1)

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 (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R26	NM_014811.5	c.-329+869G>A		intron_variant	Intron 1 of 3	ENST00000356818.7	NP_055626.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R26	ENST00000356818.7	c.-329+869G>A		intron_variant	Intron 1 of 3	1	NM_014811.5	ENSP00000349274.2

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121862 AN: 152046 Hom.: 49508 Cov.: 33

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.775

GnomAD4 exome AF: 0.765 AC: 182 AN: 238 Hom.: 69 AF XY: 0.760 AC XY: 117 AN XY: 154

African (AFR) AF: 0.900 AC: 9 AN: 10

American (AMR) AF: 1.00 AC: 2 AN: 2

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: 0.750 AC: 12 AN: 16

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.732 AC: 139 AN: 190

Other (OTH) AF: 1.00 AC: 20 AN: 20

GnomAD4 genome AF: 0.802 AC: 121987 AN: 152164 Hom.: 49575 Cov.: 33 AF XY: 0.800 AC XY: 59473 AN XY: 74374

African (AFR) AF: 0.944 AC: 39233 AN: 41574

American (AMR) AF: 0.827 AC: 12650 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3470

East Asian (EAS) AF: 0.767 AC: 3931 AN: 5128

South Asian (SAS) AF: 0.764 AC: 3680 AN: 4816

European-Finnish (FIN) AF: 0.724 AC: 7665 AN: 10592

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50340 AN: 67976

Other (OTH) AF: 0.776 AC: 1641 AN: 2114

Alfa AF: 0.750 Hom.: 43823

Bravo AF: 0.815

Asia WGS AF: 0.782 AC: 2720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.94
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs3789911; hg19: chr9-138372737;