dbSNP rs4751995: PNLIPRP2:p.Ter357Trpext*? (chr10-116638373-A-G) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 2P and 8B. PM4BA1

The ENST00000579578.6(PNLIPRP2):c.1071A>G(p.Ter357Trpext*?) variant causes a stop lost change. The variant allele was found at a frequency of 0.468 in 1,113,658 control chromosomes in the GnomAD database, including 124,765 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 0.55 ( 23011 hom., cov: 31)

Exomes 𝑓: 0.46 ( 101754 hom. )

Consequence

PNLIPRP2
ENST00000579578.6 stop_lost

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.20

Publications

32 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: Likely_benign. The variant received -6 ACMG points.

PM4

Stoplost variant in ENST00000579578.6 Downstream stopcodon found after 364 codons.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PNLIPRP2	NR_103727.2 link	n.1097A>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.1071A>G	p.Ter357Trpext*?	stop_lost	Exon 11 of 13	2		ENSP00000463502.4

Frequencies

GnomAD3 genomes

AF:

0.546

AC:

82791

AN:

151630

Hom.:

22966

Cov.:

show subpopulations

Gnomad AFR

AF:

0.621

Gnomad AMI

AF:

0.601

Gnomad AMR

AF:

0.540

Gnomad ASJ

AF:

0.493

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.406

Gnomad FIN

AF:

0.635

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.521

Gnomad OTH

AF:

0.529

GnomAD2 exomes

AF:

0.492

AC:

77564

AN:

157686

AF XY:

0.486

show subpopulations

Gnomad AFR exome

AF:

0.612

Gnomad AMR exome

AF:

0.485

Gnomad ASJ exome

AF:

0.499

Gnomad EAS exome

AF:

0.245

Gnomad FIN exome

AF:

0.630

Gnomad NFE exome

AF:

0.509

Gnomad OTH exome

AF:

0.495

GnomAD4 exome

AF:

0.456

AC:

438756

AN:

961910

Hom.:

101754

Cov.:

AF XY:

0.457

AC XY:

224958

AN XY:

492074

show subpopulations

African (AFR)

AF:

0.588

AC:

13412

AN:

22794

American (AMR)

AF:

0.494

AC:

16325

AN:

33072

Ashkenazi Jewish (ASJ)

AF:

0.489

AC:

10727

AN:

21952

East Asian (EAS)

AF:

0.266

AC:

9321

AN:

35094

South Asian (SAS)

AF:

0.401

AC:

27567

AN:

68792

European-Finnish (FIN)

AF:

0.626

AC:

30968

AN:

49504

Middle Eastern (MID)

AF:

0.479

AC:

2312

AN:

4828

European-Non Finnish (NFE)

AF:

0.451

AC:

307706

AN:

682376

Other (OTH)

AF:

0.469

AC:

20418

AN:

43498

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.435

Heterozygous variant carriers

9059

18118

27177

36236

45295

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6984

13968

20952

27936

34920

<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:

0.546

AC:

82901

AN:

151748

Hom.:

23011

Cov.:

AF XY:

0.548

AC XY:

40638

AN XY:

74152

show subpopulations

African (AFR)

AF:

0.622

AC:

25695

AN:

41304

American (AMR)

AF:

0.540

AC:

8248

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.493

AC:

1712

AN:

3472

East Asian (EAS)

AF:

0.276

AC:

1419

AN:

5150

South Asian (SAS)

AF:

0.404

AC:

1944

AN:

4808

European-Finnish (FIN)

AF:

0.635

AC:

6682

AN:

10530

Middle Eastern (MID)

AF:

0.490

AC:

143

AN:

292

European-Non Finnish (NFE)

AF:

0.521

AC:

35390

AN:

67912

Other (OTH)

AF:

0.532

AC:

1122

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1862

3724

5587

7449

9311

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

704

1408

2112

2816

3520

<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:

0.520

Hom.:

68118

Bravo

AF:

0.544

TwinsUK

AF:

0.530

AC:

1967

ALSPAC

AF:

0.519

AC:

2000

ESP6500AA

AF:

0.632

AC:

2314

ESP6500EA

AF:

0.518

AC:

4225

ExAC

AF:

0.430

AC:

47563

Asia WGS

AF:

0.445

AC:

1546

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.51

CADD

Benign

(source)

DANN

Benign

0.70

FATHMM_MKL

Benign

0.018

PhyloP100

5.2

GERP RS

5.5

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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