chr10-116461798-C-T

Variant names:

• chr10-116461798-C-T
• rs1897516
• NM_001011709.3:c.808+508C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001011709.3(PNLIPRP3):​c.808+508C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 151,958 control chromosomes in the GnomAD database, including 39,393 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 0.70 (39393 hom., cov: 31)
• Consequence: PNLIPRP3 NM_001011709.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.829 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.808+508C>T		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.808+508C>T		intron	N/A	ENSP00000358232.3

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106194 AN: 151842 Hom.: 39391 Cov.: 31

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.699 AC: 106207 AN: 151958 Hom.: 39393 Cov.: 31 AF XY: 0.695 AC XY: 51632 AN XY: 74272

African (AFR) AF: 0.483 AC: 20003 AN: 41390

American (AMR) AF: 0.622 AC: 9493 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3018 AN: 3468

East Asian (EAS) AF: 0.370 AC: 1902 AN: 5136

South Asian (SAS) AF: 0.814 AC: 3920 AN: 4816

European-Finnish (FIN) AF: 0.803 AC: 8489 AN: 10566

Middle Eastern (MID) AF: 0.846 AC: 247 AN: 292

European-Non Finnish (NFE) AF: 0.835 AC: 56748 AN: 68000

Other (OTH) AF: 0.733 AC: 1549 AN: 2112

Alfa AF: 0.635 Hom.: 2781

Bravo AF: 0.668

Asia WGS AF: 0.604 AC: 2102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.57
PhyloP100		0.45
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: rs1897516; hg19: chr10-118221310;