chr10-116638373-A-G

Variant names:

• chr10-116638373-A-G
• rs4751995
• ENST00000579578.6:c.1071A>G

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 2P and 8B. PM4 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.20
• Publications: 32 publications found

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]

ACMG classification

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	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	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.: 31

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

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.: 13 AF XY: 0.457 AC XY: 224958 AN XY: 492074

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

GnomAD4 genome AF: 0.546 AC: 82901 AN: 151748 Hom.: 23011 Cov.: 31 AF XY: 0.548 AC XY: 40638 AN XY: 74152

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

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	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	18
DANN	Benign	0.70
FATHMM_MKL	Benign	0.018	N
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

Other links and lift over

dbSNP: rs4751995; hg19: chr10-118397884; COSMIC: COSV53945236; COSMIC: COSV53945236;