10-116428026-G-T

Variant names:

• chr10-116428026-G-T
• NM_001011709.3:c.14G>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001011709.3(PNLIPRP3):​c.14G>T​(p.Trp5Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,456,814 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: PNLIPRP3 NM_001011709.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PNLIPRP3	NM_001011709.3	c.14G>T	p.Trp5Leu	missense_variant	Exon 1 of 12	ENST00000369230.4	NP_001011709.2
PNLIPRP3	XM_011539279.2	c.-147G>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 11		XP_011537581.1
PNLIPRP3	XM_011539276.2	c.14G>T	p.Trp5Leu	missense_variant	Exon 1 of 10		XP_011537578.1
PNLIPRP3	XM_011539279.2	c.-147G>T		5_prime_UTR_variant	Exon 1 of 11		XP_011537581.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PNLIPRP3	ENST00000369230.4	c.14G>T	p.Trp5Leu	missense_variant	Exon 1 of 12	1	NM_001011709.3	ENSP00000358232.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1456814 Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0 AN XY: 724808

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.02e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Uncertain	0.024	T
BayesDel_noAF	Benign	-0.20
CADD	Benign	22
DANN	Benign	0.95
DEOGEN2	Benign	0.034	T
Eigen	Benign	-0.10
Eigen_PC	Benign	-0.078
FATHMM_MKL	Benign	0.56	D
LIST_S2	Benign	0.40	T
M_CAP	Benign	0.0064	T
MetaRNN	Uncertain	0.45	T
MetaSVM	Benign	-0.62	T
MutationAssessor	Benign	0.98	L
PrimateAI	Benign	0.47	T
PROVEAN	Pathogenic	-8.0	D
REVEL	Uncertain	0.36
Sift	Benign	0.037	D
Sift4G	Benign	0.17	T
Polyphen		0.69	P
Vest4		0.42
MutPred		0.70		Gain of sheet (P = 0.0085);
MVP		0.77
MPC		0.061
ClinPred		0.74	D
GERP RS		2.0
Varity_R		0.35
gMVP		0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-118187538;