NM_001011709.3:c.1172+275C>T

Variant names:

• chr10-116472154-C-T
• rs7906587
• NM_001011709.3:c.1172+275C>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.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
• Publications: 7 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]

ENSG00000304870 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PNLIPRP3	NM_001011709.3	c.1172+275C>T		intron_variant	Intron 10 of 11	ENST00000369230.4	NP_001011709.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PNLIPRP3	ENST00000369230.4	c.1172+275C>T		intron_variant	Intron 10 of 11	1	NM_001011709.3	ENSP00000358232.3
ENSG00000304870	ENST00000806774.1	n.834G>A		non_coding_transcript_exon_variant	Exon 2 of 2

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

African (AFR) AF: 0.254 AC: 10513 AN: 41414

American (AMR) AF: 0.145 AC: 2211 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0902 AC: 313 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1293 AN: 5170

South Asian (SAS) AF: 0.0725 AC: 349 AN: 4816

European-Finnish (FIN) AF: 0.0513 AC: 542 AN: 10566

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0633 AC: 4304 AN: 67982

Other (OTH) AF: 0.0949 AC: 200 AN: 2108

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
PhyloP100		-0.25
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: rs7906587; hg19: chr10-118231666;