rs3789911

chr9-135480891-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PPP1R26	NM_014811.5	c.-329+869G>A		intron_variant		ENST00000356818.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R26	ENST00000356818.7	c.-329+869G>A		intron_variant		1	NM_014811.5	P1
PPP1R26	ENST00000604351.5	c.-196+1167G>A		intron_variant		3		P1
PPP1R26	ENST00000605286.5	c.-329+1780G>A		intron_variant		3		P1
PPP1R26	ENST00000652373.1	n.47+1167G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.900

Gnomad4 AMR exome AF: 1.00

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.732

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.776

Alfa AF: 0.747 Hom.: 33869

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs3789911; hg19: chr9-138372737;