dbSNP rs3789911: PPP1R26:c.-329+869G>A (chr9-135480891-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.408

Publications

5 publications found

Variant links:

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 links:

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

PPP1R26-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014811.5. 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
	PPP1R26	NM_014811.5	MANE Select	c.-329+869G>A		intron	N/A	NP_055626.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PPP1R26	ENST00000356818.7	TSL:1 MANE Select	c.-329+869G>A	intron	N/A	ENSP00000349274.2
PPP1R26	ENST00000604351.5	TSL:3	c.-196+1167G>A	intron	N/A	ENSP00000473820.1
PPP1R26	ENST00000605286.5	TSL:3	c.-329+1780G>A	intron	N/A	ENSP00000474807.1

Frequencies

GnomAD3 genomes

AF:

0.801

AC:

121862

AN:

152046

Hom.:

49508

Cov.:

show subpopulations

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.:

AF XY:

0.760

AC XY:

117

AN XY:

154

show subpopulations

African (AFR)

AF:

0.900

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.732

AC:

139

AN:

190

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.802

AC:

121987

AN:

152164

Hom.:

49575

Cov.:

AF XY:

0.800

AC XY:

59473

AN XY:

74374

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1205

2410

3615

4820

6025

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

868

1736

2604

3472

4340

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.7

(source)

DANN

Benign

0.94

PhyloP100

-0.41

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over