chr12-108206364-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014653.4(WSCD2):c.458A>G(p.Lys153Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000477 in 1,614,262 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K153M) has been classified as Uncertain significance.
Frequency
Consequence
NM_014653.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WSCD2 | NM_014653.4 | c.458A>G | p.Lys153Arg | missense_variant | 3/9 | ENST00000547525.6 | |
LOC124903077 | XR_007063583.1 | n.183-15345T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WSCD2 | ENST00000547525.6 | c.458A>G | p.Lys153Arg | missense_variant | 3/9 | 1 | NM_014653.4 | P1 | |
WSCD2 | ENST00000332082.8 | c.458A>G | p.Lys153Arg | missense_variant | 4/10 | 1 | P1 | ||
WSCD2 | ENST00000549903.1 | c.458A>G | p.Lys153Arg | missense_variant | 2/9 | 5 | |||
WSCD2 | ENST00000551638.5 | c.-2A>G | 5_prime_UTR_variant | 2/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000722 AC: 11AN: 152254Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000801 AC: 20AN: 249568Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135394
GnomAD4 exome AF: 0.0000451 AC: 66AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.0000330 AC XY: 24AN XY: 727244
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152372Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74512
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2023 | The c.458A>G (p.K153R) alteration is located in exon 3 (coding exon 2) of the WSCD2 gene. This alteration results from a A to G substitution at nucleotide position 458, causing the lysine (K) at amino acid position 153 to be replaced by an arginine (R). 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