rs7906587

chr10-116472154-C-T

Variant summary

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

The NM_001011709.3(PNLIPRP3):c.1172+275C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,010 control chromosomes in the GnomAD database, including 1,859 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 0.13 (1859 hom., cov: 33)
• Consequence: PNLIPRP3 NM_001011709.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PNLIPRP3	NM_001011709.3	c.1172+275C>T		intron_variant		ENST00000369230.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PNLIPRP3	ENST00000369230.4	c.1172+275C>T		intron_variant		1	NM_001011709.3	P1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19697 AN: 151892 Hom.: 1850 Cov.: 33

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0902

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.0513

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.0925

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

GnomAD4 genome AF: 0.130 AC: 19746 AN: 152010 Hom.: 1859 Cov.: 33 AF XY: 0.131 AC XY: 9716 AN XY: 74294

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0902

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.0725

Gnomad4 FIN AF: 0.0513

Gnomad4 NFE AF: 0.0633

Gnomad4 OTH AF: 0.0949

Alfa AF: 0.104 Hom.: 207

Bravo AF: 0.146

Asia WGS AF: 0.155 AC: 540 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.7
Dann	Benign	0.44

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: rs7906587; hg19: chr10-118231666;