rs764695

Positions:

• chr10-116468274-A-T

Variant summary

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

The NM_001011709.3(PNLIPRP3):​c.928-911A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,088 control chromosomes in the GnomAD database, including 2,313 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 0.14 (2313 hom., cov: 32)
• Consequence: PNLIPRP3 NM_001011709.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PNLIPRP3	NM_001011709.3	c.928-911A>T		intron_variant		ENST00000369230.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PNLIPRP3	ENST00000369230.4	c.928-911A>T		intron_variant		1	NM_001011709.3	P1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20906 AN: 151970 Hom.: 2303 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0497

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.0501

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.0932

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

GnomAD4 genome AF: 0.138 AC: 20962 AN: 152088 Hom.: 2313 Cov.: 32 AF XY: 0.138 AC XY: 10270 AN XY: 74344

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0497

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.0691

Gnomad4 FIN AF: 0.0501

Gnomad4 NFE AF: 0.0573

Gnomad4 OTH AF: 0.0956

Alfa AF: 0.101 Hom.: 162

Bravo AF: 0.156

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.70
DANN	Benign	0.80

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: rs764695; hg19: chr10-118227786; COSMIC: COSV65048801;