Genetic Variant 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. Variant has been reported in ClinVar as (no stars).

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:

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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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579578.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNLIPRP2	NR_103727.2		n.1097A>G		non_coding_transcript_exon	Exon 11 of 13

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNLIPRP2	ENST00000579578.6	TSL:2	c.1071A>G	p.Ter357Trpext*?	stop_lost	Exon 11 of 13	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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over