rs3812141
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_153362.3(PRSS35):c.984C>T(p.Ser328=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,613,828 control chromosomes in the GnomAD database, including 23,057 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.
Frequency
Genomes: 𝑓 0.18 ( 2691 hom., cov: 32)
Exomes 𝑓: 0.16 ( 20366 hom. )
Consequence
PRSS35
NM_153362.3 synonymous
NM_153362.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.34
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP7
?
Synonymous conserved (PhyloP=-3.34 with no splicing effect.
BA1
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GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRSS35 | NM_153362.3 | c.984C>T | p.Ser328= | synonymous_variant | 2/2 | ENST00000369700.4 | |
PRSS35 | NM_001170423.2 | c.984C>T | p.Ser328= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRSS35 | ENST00000369700.4 | c.984C>T | p.Ser328= | synonymous_variant | 2/2 | 1 | NM_153362.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.180 AC: 27278AN: 151848Hom.: 2689 Cov.: 32
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GnomAD3 exomes AF: 0.168 AC: 42173AN: 250956Hom.: 3972 AF XY: 0.173 AC XY: 23446AN XY: 135676
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GnomAD4 exome AF: 0.163 AC: 237954AN: 1461862Hom.: 20366 Cov.: 36 AF XY: 0.165 AC XY: 120353AN XY: 727232
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GnomAD4 genome ? AF: 0.180 AC: 27282AN: 151966Hom.: 2691 Cov.: 32 AF XY: 0.181 AC XY: 13473AN XY: 74286
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at