chr7-141836426-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001008270.3(PRSS37):āc.677C>Gā(p.Ser226Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,614,006 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000033 ( 0 hom., cov: 33)
Exomes š: 0.000029 ( 0 hom. )
Consequence
PRSS37
NM_001008270.3 missense
NM_001008270.3 missense
Scores
8
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.79
Genes affected
PRSS37 (HGNC:29211): (serine protease 37) Predicted to enable serine-type endopeptidase activity. Involved in positive regulation of acrosome reaction and regulation of protein processing. Located in acrosomal vesicle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.4184428).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRSS37 | NM_001008270.3 | c.677C>G | p.Ser226Cys | missense_variant | 5/5 | ENST00000350549.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRSS37 | ENST00000350549.8 | c.677C>G | p.Ser226Cys | missense_variant | 5/5 | 1 | NM_001008270.3 | P1 | |
PRSS37 | ENST00000452758.1 | c.*447C>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 1 | ||||
PRSS37 | ENST00000438520.1 | c.677C>G | p.Ser226Cys | missense_variant | 6/6 | 5 | P1 | ||
PRSS37 | ENST00000419085.5 | c.*1451C>G | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152128Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251478Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135910
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GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461878Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 727238
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152128Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74294
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
D;D
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
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MPC
ClinPred
D
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at