4-151277198-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_183375.5(PRSS48):c.26C>T(p.Thr9Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000666 in 1,501,324 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_183375.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRSS48 | NM_183375.5 | c.26C>T | p.Thr9Met | missense_variant | Exon 1 of 5 | ENST00000455694.7 | NP_899231.4 | |
SH3D19 | NM_001378122.1 | c.112+48043G>A | intron_variant | Intron 1 of 19 | ENST00000604030.7 | NP_001365051.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRSS48 | ENST00000455694.7 | c.26C>T | p.Thr9Met | missense_variant | Exon 1 of 5 | 1 | NM_183375.5 | ENSP00000401328.2 | ||
PRSS48 | ENST00000441586.2 | c.26C>T | p.Thr9Met | missense_variant | Exon 1 of 3 | 1 | ENSP00000401420.2 | |||
SH3D19 | ENST00000604030.7 | c.112+48043G>A | intron_variant | Intron 1 of 19 | 5 | NM_001378122.1 | ENSP00000488951.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000140 AC: 3AN: 213586Hom.: 0 AF XY: 0.0000171 AC XY: 2AN XY: 116734
GnomAD4 exome AF: 0.0000682 AC: 92AN: 1349152Hom.: 0 Cov.: 30 AF XY: 0.0000613 AC XY: 41AN XY: 668930
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74332
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at