rs764695

Variant names:

• chr10-116468274-A-T
• rs764695
• NM_001011709.3:c.928-911A>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.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
• Publications: 2 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=-0.91).
• 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 rank	MANE	Protein	UniProt
PNLIPRP3	NM_001011709.3	c.928-911A>T		intron_variant	Intron 8 of 11	ENST00000369230.4	NP_001011709.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PNLIPRP3	ENST00000369230.4	c.928-911A>T		intron_variant	Intron 8 of 11	1	NM_001011709.3	ENSP00000358232.3

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

African (AFR) AF: 0.297 AC: 12304 AN: 41440

American (AMR) AF: 0.145 AC: 2209 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0497 AC: 172 AN: 3464

East Asian (EAS) AF: 0.251 AC: 1299 AN: 5180

South Asian (SAS) AF: 0.0691 AC: 332 AN: 4806

European-Finnish (FIN) AF: 0.0501 AC: 530 AN: 10586

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0573 AC: 3900 AN: 68010

Other (OTH) AF: 0.0956 AC: 202 AN: 2114

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
PhyloP100		-0.052
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: rs764695; hg19: chr10-118227786; COSMIC: COSV65048801;