rs10885997

Positions:

• chr10-116638460-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The ENST00000579578.6(PNLIPRP2):​c.1158A>G​(p.Ser386=) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PNLIPRP2	NR_103727.2	n.1184A>G		non_coding_transcript_exon_variant	11/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PNLIPRP2	ENST00000579578.6	c.1158A>G	p.Ser386=	synonymous_variant	11/13	2		ENSP00000463502	P1

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54990 AN: 151926 Hom.: 10792 Cov.: 32

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

GnomAD3 exomes AF: 0.384 AC: 63506 AN: 165350 Hom.: 12826 AF XY: 0.381 AC XY: 33111 AN XY: 86954

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 SAS exome AF: 0.335

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.: 17 AF XY: 0.377 AC XY: 223676 AN XY: 592644

Gnomad4 AFR exome AF: 0.204

Gnomad4 AMR exome AF: 0.401

Gnomad4 ASJ exome AF: 0.399

Gnomad4 EAS exome AF: 0.268

Gnomad4 SAS exome AF: 0.325

Gnomad4 FIN exome AF: 0.536

Gnomad4 NFE exome AF: 0.382

Gnomad4 OTH exome AF: 0.368

GnomAD4 genome AF: 0.362 AC: 55028 AN: 152044 Hom.: 10797 Cov.: 32 AF XY: 0.368 AC XY: 27374 AN XY: 74298

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.375

Alfa AF: 0.387 Hom.: 11407

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
DANN	Benign	0.74

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

LitVar

Other links and lift over

dbSNP: rs10885997; hg19: chr10-118397971; COSMIC: COSV53947738; COSMIC: COSV53947738;