Variant 16-31087690-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001039503.3(PRSS53):c.89A>G(p.Gln30Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.051 in 1,612,712 control chromosomes in the GnomAD database, including 17,080 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.

Frequency

Genomes: 𝑓 0.060 ( 1886 hom., cov: 33)

Exomes 𝑓: 0.050 ( 15194 hom. )

Consequence

PRSS53
NM_001039503.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.64

Variant links:

Genes affected

PRSS53 (HGNC:34407): (serine protease 53) Predicted to enable serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

PRSS53 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=1.1534233E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRSS53	NM_001039503.3 linkuse as main transcript	c.89A>G	p.Gln30Arg	missense_variant	3/11	ENST00000280606.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
PRSS53	ENST00000280606.7 linkuse as main transcript	c.89A>G	p.Gln30Arg	missense_variant	3/11	1	NM_001039503.3	P1
PRSS53	ENST00000486499.1 linkuse as main transcript	n.1939A>G		non_coding_transcript_exon_variant	1/2	2
PRSS53	ENST00000492427.2 linkuse as main transcript	n.1039A>G		non_coding_transcript_exon_variant	1/4	3

Frequencies

GnomAD3 genomes

AF:

0.0600

AC:

9130

AN:

152170

Hom.:

1885

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0110

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.0138

Gnomad EAS

AF:

0.788

Gnomad SAS

AF:

0.0341

Gnomad FIN

AF:

0.0789

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0178

Gnomad OTH

AF:

0.0660

GnomAD3 exomes

AF:

0.118

AC:

28877

AN:

245378

Hom.:

7269

AF XY:

0.102

AC XY:

13624

AN XY:

133320

show subpopulations

Gnomad AFR exome

AF:

0.0107

Gnomad AMR exome

AF:

0.284

Gnomad ASJ exome

AF:

0.0113

Gnomad EAS exome

AF:

0.797

Gnomad SAS exome

AF:

0.0198

Gnomad FIN exome

AF:

0.0777

Gnomad NFE exome

AF:

0.0192

Gnomad OTH exome

AF:

0.0798

GnomAD4 exome

AF:

0.0501

AC:

73103

AN:

1460424

Hom.:

15194

Cov.:

AF XY:

0.0478

AC XY:

34687

AN XY:

726398

show subpopulations

Gnomad4 AFR exome

AF:

0.00661

Gnomad4 AMR exome

AF:

0.271

Gnomad4 ASJ exome

AF:

0.0111

Gnomad4 EAS exome

AF:

0.789

Gnomad4 SAS exome

AF:

0.0210

Gnomad4 FIN exome

AF:

0.0776

Gnomad4 NFE exome

AF:

0.0172

Gnomad4 OTH exome

AF:

0.0690

GnomAD4 genome

AF:

0.0600

AC:

9131

AN:

152288

Hom.:

1886

Cov.:

AF XY:

0.0664

AC XY:

4944

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.0109

Gnomad4 AMR

AF:

0.144

Gnomad4 ASJ

AF:

0.0138

Gnomad4 EAS

AF:

0.788

Gnomad4 SAS

AF:

0.0333

Gnomad4 FIN

AF:

0.0789

Gnomad4 NFE

AF:

0.0178

Gnomad4 OTH

AF:

0.0658

Alfa

AF:

0.0332

Hom.:

1558

Bravo

AF:

0.0729

TwinsUK

AF:

0.0129

AC:

ALSPAC

AF:

0.0174

AC:

ESP6500AA

AF:

0.0127

AC:

ESP6500EA

AF:

0.0176

AC:

147

ExAC

AF:

0.106

AC:

12811

Asia WGS

AF:

0.326

AC:

1130

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.072

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.35

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0075

T;.

Eigen

Benign

-0.39

Eigen_PC

Benign

-0.12

FATHMM_MKL

Benign

0.68

LIST_S2

Benign

0.71

T;T

MetaRNN

Benign

0.0000012

T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

-0.19

N;.

MutationTaster

Benign

0.85

PrimateAI

Benign

0.40

PROVEAN

Benign

0.32

N;N

REVEL

Benign

0.19

Sift

Benign

0.44

T;T

Sift4G

Benign

0.12

T;T

Polyphen

0.14

B;.

Vest4

0.17

MPC

0.27

ClinPred

0.014

GERP RS

6.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.064

gMVP

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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