dbSNP rs11892119: PPIL3:n.789A>G (chr2-200871389-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000465823.5(PPIL3):n.789A>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 0.128 in 1,604,924 control chromosomes in the GnomAD database, including 16,139 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 0.19 ( 3711 hom., cov: 31)

Exomes 𝑓: 0.12 ( 12428 hom. )

Consequence

PPIL3
ENST00000465823.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.602

Publications

19 publications found

Variant links:

Genes affected

PPIL3 (HGNC:9262): (peptidylprolyl isomerase like 3) This gene encodes a member of the cyclophilin family. Cyclophilins catalyze the cis-trans isomerization of peptidylprolyl imide bonds in oligopeptides. They have been proposed to act either as catalysts or as molecular chaperones in protein-folding events. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2008]

PPIL3 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=-0.67).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIL3	NM_130906.3 link	c.*6A>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000392283.9	NP_570981.1	Q9H2H8-1A0A024R3V4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIL3	ENST00000392283.9 link	c.*6A>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_130906.3	ENSP00000376107.4		Q9H2H8-1

Frequencies

GnomAD3 genomes

AF:

0.187

AC:

28479

AN:

151984

Hom.:

3703

Cov.:

show subpopulations

Gnomad AFR

AF:

0.370

Gnomad AMI

AF:

0.120

Gnomad AMR

AF:

0.136

Gnomad ASJ

AF:

0.149

Gnomad EAS

AF:

0.00768

Gnomad SAS

AF:

0.0507

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.115

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.178

GnomAD2 exomes

AF:

0.117

AC:

28925

AN:

247530

AF XY:

0.112

show subpopulations

Gnomad AFR exome

AF:

0.385

Gnomad AMR exome

AF:

0.0781

Gnomad ASJ exome

AF:

0.132

Gnomad EAS exome

AF:

0.00453

Gnomad FIN exome

AF:

0.107

Gnomad NFE exome

AF:

0.125

Gnomad OTH exome

AF:

0.118

GnomAD4 exome

AF:

0.121

AC:

176302

AN:

1452822

Hom.:

12428

Cov.:

AF XY:

0.119

AC XY:

86081

AN XY:

722920

show subpopulations

African (AFR)

AF:

0.378

AC:

12471

AN:

33008

American (AMR)

AF:

0.0850

AC:

3698

AN:

43500

Ashkenazi Jewish (ASJ)

AF:

0.137

AC:

3551

AN:

25980

East Asian (EAS)

AF:

0.00250

AC:

AN:

39568

South Asian (SAS)

AF:

0.0561

AC:

4777

AN:

85084

European-Finnish (FIN)

AF:

0.107

AC:

5706

AN:

53320

Middle Eastern (MID)

AF:

0.133

AC:

765

AN:

5744

European-Non Finnish (NFE)

AF:

0.124

AC:

137552

AN:

1106576

Other (OTH)

AF:

0.128

AC:

7683

AN:

60042

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.451

Heterozygous variant carriers

6952

13905

20857

27810

34762

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4930

9860

14790

19720

24650

<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:

0.188

AC:

28525

AN:

152102

Hom.:

3711

Cov.:

AF XY:

0.183

AC XY:

13578

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.370

AC:

15344

AN:

41440

American (AMR)

AF:

0.136

AC:

2077

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.149

AC:

517

AN:

3468

East Asian (EAS)

AF:

0.00770

AC:

AN:

5194

South Asian (SAS)

AF:

0.0505

AC:

244

AN:

4828

European-Finnish (FIN)

AF:

0.101

AC:

1067

AN:

10586

Middle Eastern (MID)

AF:

0.113

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.128

AC:

8722

AN:

68006

Other (OTH)

AF:

0.176

AC:

372

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1057

2113

3170

4226

5283

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

284

568

852

1136

1420

<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:

0.152

Hom.:

2233

Bravo

AF:

0.200

Asia WGS

AF:

0.0630

AC:

220

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

(source)

DANN

Benign

0.78

PhyloP100

0.60

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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