16-31084843-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001039503.3(PRSS53):​c.1216C>T​(p.Pro406Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 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: 34)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PRSS53
NM_001039503.3 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.410
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.02690646).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PRSS53NM_001039503.3 linkuse as main transcriptc.1216C>T p.Pro406Ser missense_variant 8/11 ENST00000280606.7 NP_001034592.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PRSS53ENST00000280606.7 linkuse as main transcriptc.1216C>T p.Pro406Ser missense_variant 8/111 NM_001039503.3 ENSP00000280606 P1
PRSS53ENST00000486499.1 linkuse as main transcriptn.4083C>T non_coding_transcript_exon_variant 2/22

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1398720
Hom.:
0
Cov.:
57
AF XY:
0.00
AC XY:
0
AN XY:
689776
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.064
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
3.3
DANN
Benign
0.93
DEOGEN2
Benign
0.072
T
Eigen
Benign
-1.4
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.057
N
LIST_S2
Benign
0.14
T
M_CAP
Benign
0.020
T
MetaRNN
Benign
0.027
T
MetaSVM
Benign
-0.84
T
MutationAssessor
Benign
0.045
N
MutationTaster
Benign
1.0
P
PrimateAI
Benign
0.36
T
PROVEAN
Benign
-0.10
N
REVEL
Benign
0.10
Sift
Benign
0.68
T
Sift4G
Benign
0.40
T
Polyphen
0.0
B
Vest4
0.084
MutPred
0.37
Loss of stability (P = 0.0863);
MVP
0.14
MPC
0.061
ClinPred
0.046
T
GERP RS
-3.0
Varity_R
0.061
gMVP
0.26

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.

Other links and lift over

dbSNP: rs7199949; hg19: chr16-31096164; API