Genetic Variant PPP1R3B-DT:n.14A>G (chr8-9325848-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000647924.2(PPP1R3B-DT):n.14A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,282 control chromosomes in the GnomAD database, including 58,460 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 0.87 ( 58451 hom., cov: 33)

Exomes 𝑓: 1.0 ( 9 hom. )

Consequence

PPP1R3B-DT
ENST00000647924.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.603

Publications

151 publications found

Variant links:

Genes affected

PPP1R3B-DT (HGNC:56150): (PPP1R3B divergent transcript)

PPP1R3B-DT links:

LOC157273 (HGNC:):

LOC157273 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC157273	NR_040039.1 link	n.364-54A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PPP1R3B-DT	ENST00000647924.2 link	n.14A>G	non_coding_transcript_exon_variant	Exon 1 of 5
PPP1R3B-DT	ENST00000649984.4 link	n.44A>G	non_coding_transcript_exon_variant	Exon 1 of 4
PPP1R3B-DT	ENST00000693061.3 link	n.279A>G	non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.874

AC:

133032

AN:

152146

Hom.:

58432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.812

Gnomad AMI

AF:

0.997

Gnomad AMR

AF:

0.829

Gnomad ASJ

AF:

0.944

Gnomad EAS

AF:

0.987

Gnomad SAS

AF:

0.892

Gnomad FIN

AF:

0.837

Gnomad MID

AF:

0.934

Gnomad NFE

AF:

0.913

Gnomad OTH

AF:

0.880

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Age Distribution

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:

0.874

AC:

133109

AN:

152264

Hom.:

58451

Cov.:

AF XY:

0.871

AC XY:

64819

AN XY:

74448

show subpopulations

African (AFR)

AF:

0.812

AC:

33726

AN:

41528

American (AMR)

AF:

0.829

AC:

12684

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.944

AC:

3276

AN:

3472

East Asian (EAS)

AF:

0.988

AC:

5118

AN:

5182

South Asian (SAS)

AF:

0.891

AC:

4304

AN:

4828

European-Finnish (FIN)

AF:

0.837

AC:

8883

AN:

10608

Middle Eastern (MID)

AF:

0.929

AC:

273

AN:

294

European-Non Finnish (NFE)

AF:

0.913

AC:

62085

AN:

68024

Other (OTH)

AF:

0.876

AC:

1851

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

867

1735

2602

3470

4337

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

900

1800

2700

3600

4500

<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:

0.897

Hom.:

111150

Bravo

AF:

0.868

Asia WGS

AF:

0.918

AC:

3195

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.0

(source)

DANN

Benign

0.58

PhyloP100

-0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over