12-108206378-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014653.4(WSCD2):c.472C>T(p.Arg158Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,614,108 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014653.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WSCD2 | ENST00000547525.6 | c.472C>T | p.Arg158Cys | missense_variant | Exon 3 of 9 | 1 | NM_014653.4 | ENSP00000448047.1 | ||
WSCD2 | ENST00000332082.8 | c.472C>T | p.Arg158Cys | missense_variant | Exon 4 of 10 | 1 | ENSP00000331933.4 | |||
WSCD2 | ENST00000549903.1 | c.472C>T | p.Arg158Cys | missense_variant | Exon 2 of 9 | 5 | ENSP00000447272.1 | |||
WSCD2 | ENST00000551638.5 | c.13C>T | p.Arg5Cys | missense_variant | Exon 2 of 5 | 4 | ENSP00000446744.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.472C>T (p.R158C) alteration is located in exon 3 (coding exon 2) of the WSCD2 gene. This alteration results from a C to T substitution at nucleotide position 472, causing the arginine (R) at amino acid position 158 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at