Variant rs11197744 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_006229.4(PNLIPRP1):c.181A>G(p.Asn61Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0257 in 1,614,070 control chromosomes in the GnomAD database, including 644 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.019 ( 53 hom., cov: 32)

Exomes 𝑓: 0.026 ( 591 hom. )

Consequence

PNLIPRP1
NM_006229.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.20

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:

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=0.0066432655).

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0195 (2967/152270) while in subpopulation NFE AF= 0.0274 (1861/68008). AF 95% confidence interval is 0.0263. There are 53 homozygotes in gnomad4. There are 1463 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 53 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
PNLIPRP1	NM_006229.4 linkuse as main transcript	c.181A>G	p.Asn61Asp	missense_variant	3/13	ENST00000358834.9
PNLIPRP1	NM_001303135.1 linkuse as main transcript	c.181A>G	p.Asn61Asp	missense_variant	3/13
PNLIPRP1	XM_047425364.1 linkuse as main transcript	c.181A>G	p.Asn61Asp	missense_variant	3/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PNLIPRP1	ENST00000358834.9 linkuse as main transcript	c.181A>G	p.Asn61Asp	missense_variant	3/13	1	NM_006229.4	P4	P54315-1

Frequencies

GnomAD3 genomes

AF:

0.0195

AC:

2969

AN:

152152

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00432

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0153

Gnomad ASJ

AF:

0.0104

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0273

Gnomad FIN

AF:

0.0445

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0274

Gnomad OTH

AF:

0.0182

GnomAD3 exomes

AF:

0.0229

AC:

5739

AN:

251106

Hom.:

AF XY:

0.0244

AC XY:

3313

AN XY:

135730

show subpopulations

Gnomad AFR exome

AF:

0.00419

Gnomad AMR exome

AF:

0.00836

Gnomad ASJ exome

AF:

0.0100

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0298

Gnomad FIN exome

AF:

0.0473

Gnomad NFE exome

AF:

0.0281

Gnomad OTH exome

AF:

0.0248

GnomAD4 exome

AF:

0.0264

AC:

38580

AN:

1461800

Hom.:

591

Cov.:

AF XY:

0.0269

AC XY:

19537

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.00350

Gnomad4 AMR exome

AF:

0.00924

Gnomad4 ASJ exome

AF:

0.00953

Gnomad4 EAS exome

AF:

0.000176

Gnomad4 SAS exome

AF:

0.0288

Gnomad4 FIN exome

AF:

0.0456

Gnomad4 NFE exome

AF:

0.0283

Gnomad4 OTH exome

AF:

0.0216

GnomAD4 genome

AF:

0.0195

AC:

2967

AN:

152270

Hom.:

Cov.:

AF XY:

0.0196

AC XY:

1463

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.00431

Gnomad4 AMR

AF:

0.0153

Gnomad4 ASJ

AF:

0.0104

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0274

Gnomad4 FIN

AF:

0.0445

Gnomad4 NFE

AF:

0.0274

Gnomad4 OTH

AF:

0.0180

Alfa

AF:

0.0245

Hom.:

Bravo

AF:

0.0160

TwinsUK

AF:

0.0259

AC:

ALSPAC

AF:

0.0330

AC:

127

ESP6500AA

AF:

0.00409

AC:

ESP6500EA

AF:

0.0283

AC:

243

ExAC

AF:

0.0235

AC:

2857

Asia WGS

AF:

0.00722

AC:

AN:

3478

EpiCase

AF:

0.0275

EpiControl

AF:

0.0256

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.35

BayesDel_noAF

Benign

-0.25

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.64

D;D;D;.;D;D;.

Eigen

Pathogenic

0.71

Eigen_PC

Pathogenic

0.68

FATHMM_MKL

Uncertain

0.95

LIST_S2

Benign

0.54

T;.;T;T;T;T;T

MetaRNN

Benign

0.0066

T;T;T;T;T;T;T

MetaSVM

Uncertain

0.59

MutationAssessor

Benign

1.9

.;L;L;.;.;.;.

MutationTaster

Benign

0.58

D;D;D;D

PrimateAI

Benign

0.37

PROVEAN

Uncertain

-3.8

D;D;D;D;D;D;D

REVEL

Uncertain

0.41

Sift

Benign

0.049

D;D;D;D;D;T;D

Sift4G

Uncertain

0.0020

D;D;D;D;D;D;D

Polyphen

0.95

.;P;P;.;.;.;.

Vest4

0.13, 0.13

MPC

0.18

ClinPred

0.034

GERP RS

5.7

Varity_R

0.49

gMVP

0.58

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