rs776563968
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001308209.2(PRSS57):c.89G>T(p.Gly30Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000033 in 1,544,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001308209.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRSS57 | ENST00000329267.9 | c.89G>T | p.Gly30Val | missense_variant | Exon 2 of 5 | 1 | NM_001308209.2 | ENSP00000327386.6 | ||
PRSS57 | ENST00000613411.4 | c.92G>T | p.Gly31Val | missense_variant | Exon 2 of 5 | 1 | ENSP00000482358.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152120Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000193 AC: 33AN: 171216Hom.: 0 AF XY: 0.000128 AC XY: 12AN XY: 93960
GnomAD4 exome AF: 0.0000323 AC: 45AN: 1392740Hom.: 0 Cov.: 31 AF XY: 0.0000218 AC XY: 15AN XY: 688396
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152238Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4AN XY: 74432
ClinVar
Submissions by phenotype
Long QT syndrome Benign:1
Likely benign, no assertion criteria provided | research | Medical Research Institute, Tokyo Medical and Dental University | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at