Genetic Variant PNLIPRP2:p.Ser386Ser (chr10-116638460-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000579578.6(PNLIPRP2):c.1158A>G(p.Ser386Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 1,331,620 control chromosomes in the GnomAD database, including 97,322 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 0.36 ( 10797 hom., cov: 32)

Exomes 𝑓: 0.38 ( 86525 hom. )

Consequence

PNLIPRP2
ENST00000579578.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.493

Publications

36 publications found

Variant links:

Genes affected

PNLIPRP2 (HGNC:9157): (pancreatic lipase related protein 2 (gene/pseudogene)) This gene encodes a lipase that hydrolyzes galactolipids, the main components of plant membrane lipids. An allelic polymorphism in this gene results in both coding and non-coding variants; the reference genome represents the non-coding allele. [provided by RefSeq, Aug 2015]

PNLIPRP2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP7

Synonymous conserved (PhyloP=0.493 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PNLIPRP2	NR_103727.2 link	n.1184A>G		non_coding_transcript_exon_variant	Exon 11 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PNLIPRP2	ENST00000579578.6 link	c.1158A>G	p.Ser386Ser	synonymous_variant	Exon 11 of 13	2		ENSP00000463502.4

Frequencies

GnomAD3 genomes

AF:

0.362

AC:

54990

AN:

151926

Hom.:

10792

Cov.:

show subpopulations

Gnomad AFR

AF:

0.222

Gnomad AMI

AF:

0.517

Gnomad AMR

AF:

0.420

Gnomad ASJ

AF:

0.397

Gnomad EAS

AF:

0.274

Gnomad SAS

AF:

0.335

Gnomad FIN

AF:

0.544

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.410

Gnomad OTH

AF:

0.370

GnomAD2 exomes

AF:

0.384

AC:

63506

AN:

165350

AF XY:

0.381

show subpopulations

Gnomad AFR exome

AF:

0.210

Gnomad AMR exome

AF:

0.401

Gnomad ASJ exome

AF:

0.405

Gnomad EAS exome

AF:

0.249

Gnomad FIN exome

AF:

0.542

Gnomad NFE exome

AF:

0.400

Gnomad OTH exome

AF:

0.381

GnomAD4 exome

AF:

0.377

AC:

444895

AN:

1179576

Hom.:

86525

Cov.:

AF XY:

0.377

AC XY:

223676

AN XY:

592644

show subpopulations

African (AFR)

AF:

0.204

AC:

5772

AN:

28330

American (AMR)

AF:

0.401

AC:

13984

AN:

34862

Ashkenazi Jewish (ASJ)

AF:

0.399

AC:

9394

AN:

23518

East Asian (EAS)

AF:

0.268

AC:

9765

AN:

36446

South Asian (SAS)

AF:

0.325

AC:

23937

AN:

73630

European-Finnish (FIN)

AF:

0.536

AC:

26686

AN:

49832

Middle Eastern (MID)

AF:

0.343

AC:

1808

AN:

5270

European-Non Finnish (NFE)

AF:

0.382

AC:

334843

AN:

876840

Other (OTH)

AF:

0.368

AC:

18706

AN:

50848

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.449

Heterozygous variant carriers

10433

20866

31298

41731

52164

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9478

18956

28434

37912

47390

<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:

0.362

AC:

55028

AN:

152044

Hom.:

10797

Cov.:

AF XY:

0.368

AC XY:

27374

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.222

AC:

9218

AN:

41484

American (AMR)

AF:

0.421

AC:

6425

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.397

AC:

1380

AN:

3472

East Asian (EAS)

AF:

0.275

AC:

1420

AN:

5170

South Asian (SAS)

AF:

0.335

AC:

1614

AN:

4818

European-Finnish (FIN)

AF:

0.544

AC:

5741

AN:

10554

Middle Eastern (MID)

AF:

0.323

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.410

AC:

27875

AN:

67958

Other (OTH)

AF:

0.375

AC:

791

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1720

3440

5159

6879

8599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<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:

0.377

Hom.:

17938

Bravo

AF:

0.347

Asia WGS

AF:

0.387

AC:

1342

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

5.7

(source)

DANN

Benign

0.74

PhyloP100

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over