rs6601483
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_198464.4(PRSS55):āc.810A>Cā(p.Ile270=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 1,613,812 control chromosomes in the GnomAD database, including 335,908 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: š 0.64 ( 30939 hom., cov: 32)
Exomes š: 0.64 ( 304969 hom. )
Consequence
PRSS55
NM_198464.4 synonymous
NM_198464.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.551
Genes affected
PRSS55 (HGNC:30824): (serine protease 55) This gene encodes a member of a group of membrane-anchored chymotrypsin (S1)-like serine proteases. The enocoded protein is primarily expressed in the Leydig and Sertoli cells of the testis and may be involved in male fertility. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2010]
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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=-0.61).
BP7
Synonymous conserved (PhyloP=0.551 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRSS55 | NM_198464.4 | c.810A>C | p.Ile270= | synonymous_variant | 5/5 | ENST00000328655.8 | |
PRSS51 | XR_007060820.1 | n.294+8886T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRSS55 | ENST00000328655.8 | c.810A>C | p.Ile270= | synonymous_variant | 5/5 | 1 | NM_198464.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.636 AC: 96621AN: 151966Hom.: 30880 Cov.: 32
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GnomAD3 exomes AF: 0.649 AC: 163036AN: 251398Hom.: 53345 AF XY: 0.647 AC XY: 87968AN XY: 135876
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GnomAD4 exome AF: 0.645 AC: 942144AN: 1461728Hom.: 304969 Cov.: 54 AF XY: 0.644 AC XY: 468282AN XY: 727176
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GnomAD4 genome AF: 0.636 AC: 96744AN: 152084Hom.: 30939 Cov.: 32 AF XY: 0.639 AC XY: 47476AN XY: 74346
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Not reported inComputational scores
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Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at