rs4751971

Positions:

• chr10-116459423-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001011709.3(PNLIPRP3):​c.566-1543G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0799 in 151,876 control chromosomes in the GnomAD database, including 1,484 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 0.080 (1484 hom., cov: 32)
• Consequence: PNLIPRP3 NM_001011709.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

Genes affected

PNLIPRP3 (HGNC:23492): (pancreatic lipase related protein 3) Predicted to enable triglyceride lipase activity. Predicted to be involved in lipid catabolic process. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PNLIPRP3	NM_001011709.3	c.566-1543G>A		intron_variant		ENST00000369230.4	NP_001011709.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PNLIPRP3	ENST00000369230.4	c.566-1543G>A		intron_variant		1	NM_001011709.3	ENSP00000358232.3

Frequencies

GnomAD3 genomes AF: 0.0797 AC: 12096 AN: 151756 Hom.: 1469 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.0774

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.00679

Gnomad OTH AF: 0.0943

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0799 AC: 12130 AN: 151876 Hom.: 1484 Cov.: 32 AF XY: 0.0878 AC XY: 6512 AN XY: 74180

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.0144

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.0300

Gnomad4 FIN AF: 0.0774

Gnomad4 NFE AF: 0.00678

Gnomad4 OTH AF: 0.0952

Alfa AF: 0.0342 Hom.: 599

Bravo AF: 0.101

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs4751971; hg19: chr10-118218935;