chr16-2784793-C-A
Position:
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_152891.3(PRSS33):c.694G>T(p.Gly232Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000413 in 1,454,388 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
PRSS33
NM_152891.3 missense
NM_152891.3 missense
Scores
15
2
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.35
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.987
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRSS33 | NM_152891.3 | c.694G>T | p.Gly232Trp | missense_variant | 7/7 | ENST00000682474.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRSS33 | ENST00000682474.1 | c.694G>T | p.Gly232Trp | missense_variant | 7/7 | NM_152891.3 | P1 | ||
PRSS33 | ENST00000293851.9 | c.694G>T | p.Gly232Trp | missense_variant | 6/6 | 1 | P1 | ||
PRSS33 | ENST00000570702.5 | c.694G>T | p.Gly232Trp | missense_variant | 7/7 | 1 | P1 | ||
PRSS33 | ENST00000576886.5 | c.*273G>T | 3_prime_UTR_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000413 AC: 6AN: 1454388Hom.: 0 Cov.: 32 AF XY: 0.00000553 AC XY: 4AN XY: 722906
GnomAD4 exome
AF:
AC:
6
AN:
1454388
Hom.:
Cov.:
32
AF XY:
AC XY:
4
AN XY:
722906
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Pathogenic
D;D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
H;H
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;.
REVEL
Pathogenic
Sift
Pathogenic
D;.
Sift4G
Pathogenic
D;D
Polyphen
D;D
Vest4
MutPred
Loss of disorder (P = 0.0079);Loss of disorder (P = 0.0079);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at