Variant rs2305204 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006229.4(PNLIPRP1):c.1242G>C(p.Glu414Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0747 in 1,610,726 control chromosomes in the GnomAD database, including 7,459 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.065 ( 701 hom., cov: 33)

Exomes 𝑓: 0.076 ( 6758 hom. )

Consequence

PNLIPRP1
NM_006229.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.470

Variant links:

Genes affected

PNLIPRP1 (HGNC:9156): (pancreatic lipase related protein 1) Predicted to enable calcium ion binding activity. Predicted to be involved in lipid catabolic process. Predicted to be located in extracellular region. Biomarker of prostate cancer. [provided by Alliance of Genome Resources, Apr 2022]

PNLIPRP1 links:

LOC124902510 (HGNC:):

LOC124902510 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.003960341).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
PNLIPRP1	NM_006229.4 linkuse as main transcript	c.1242G>C	p.Glu414Asp	missense_variant	12/13	ENST00000358834.9
LOC124902510	XR_007062299.1 linkuse as main transcript	n.1932C>G		non_coding_transcript_exon_variant	2/2
PNLIPRP1	NM_001303135.1 linkuse as main transcript	c.1242G>C	p.Glu414Asp	missense_variant	12/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PNLIPRP1	ENST00000358834.9 linkuse as main transcript	c.1242G>C	p.Glu414Asp	missense_variant	12/13	1	NM_006229.4	P4	P54315-1

Frequencies

GnomAD3 genomes

AF:

0.0648

AC:

9857

AN:

152054

Hom.:

705

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0156

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0508

Gnomad ASJ

AF:

0.0818

Gnomad EAS

AF:

0.408

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.0678

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.0661

Gnomad OTH

AF:

0.0789

GnomAD3 exomes

AF:

0.0930

AC:

23354

AN:

251198

Hom.:

2398

AF XY:

0.0944

AC XY:

12816

AN XY:

135772

show subpopulations

Gnomad AFR exome

AF:

0.0150

Gnomad AMR exome

AF:

0.0442

Gnomad ASJ exome

AF:

0.0733

Gnomad EAS exome

AF:

0.442

Gnomad SAS exome

AF:

0.103

Gnomad FIN exome

AF:

0.0667

Gnomad NFE exome

AF:

0.0668

Gnomad OTH exome

AF:

0.0920

GnomAD4 exome

AF:

0.0757

AC:

110477

AN:

1458554

Hom.:

6758

Cov.:

AF XY:

0.0765

AC XY:

55481

AN XY:

725610

show subpopulations

Gnomad4 AFR exome

AF:

0.0155

Gnomad4 AMR exome

AF:

0.0457

Gnomad4 ASJ exome

AF:

0.0796

Gnomad4 EAS exome

AF:

0.399

Gnomad4 SAS exome

AF:

0.102

Gnomad4 FIN exome

AF:

0.0667

Gnomad4 NFE exome

AF:

0.0645

Gnomad4 OTH exome

AF:

0.0923

GnomAD4 genome

AF:

0.0647

AC:

9851

AN:

152172

Hom.:

701

Cov.:

AF XY:

0.0674

AC XY:

5016

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.0157

Gnomad4 AMR

AF:

0.0506

Gnomad4 ASJ

AF:

0.0818

Gnomad4 EAS

AF:

0.407

Gnomad4 SAS

AF:

0.121

Gnomad4 FIN

AF:

0.0678

Gnomad4 NFE

AF:

0.0662

Gnomad4 OTH

AF:

0.0823

Alfa

AF:

0.0748

Hom.:

517

Bravo

AF:

0.0643

TwinsUK

AF:

0.0653

AC:

242

ALSPAC

AF:

0.0646

AC:

249

ESP6500AA

AF:

0.0188

AC:

ESP6500EA

AF:

0.0686

AC:

590

ExAC

AF:

0.0930

AC:

11295

Asia WGS

AF:

0.223

AC:

775

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0094

T;T;.

Eigen

Benign

-0.28

Eigen_PC

Benign

-0.099

FATHMM_MKL

Benign

0.68

LIST_S2

Benign

0.49

.;T;T

MetaRNN

Benign

0.0040

T;T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

1.5

L;L;.

MutationTaster

Benign

0.99

P;P;P

PrimateAI

Benign

0.35

PROVEAN

Benign

-1.2

N;N;N

REVEL

Benign

0.058

Sift

Benign

0.41

T;T;T

Sift4G

Benign

0.60

T;T;T

Polyphen

0.0

B;B;.

Vest4

0.032

MutPred

0.19

Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);

MPC

0.038

ClinPred

0.0068

GERP RS

4.6

Varity_R

0.11

gMVP

0.28

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over