10-116459423-G-A

Variant names:

• chr10-116459423-G-A
• rs4751971
• NM_001011709.3:c.566-1543G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001011709.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNLIPRP3	NM_001011709.3	MANE Select	c.566-1543G>A		intron	N/A	NP_001011709.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNLIPRP3	ENST00000369230.4	TSL:1 MANE Select	c.566-1543G>A		intron	N/A	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

African (AFR) AF: 0.101 AC: 4198 AN: 41396

American (AMR) AF: 0.247 AC: 3768 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3470

East Asian (EAS) AF: 0.485 AC: 2485 AN: 5120

South Asian (SAS) AF: 0.0300 AC: 144 AN: 4800

European-Finnish (FIN) AF: 0.0774 AC: 816 AN: 10540

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.00678 AC: 461 AN: 67990

Other (OTH) AF: 0.0952 AC: 200 AN: 2100

Alfa AF: 0.0418 Hom.: 856

Bravo AF: 0.101

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.57
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4751971; hg19: chr10-118218935;