chrX-10109915-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_015691.5(WWC3):c.1241A>G(p.Gln414Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000331 in 1,208,768 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. Q414Q) has been classified as Benign.
Frequency
Consequence
NM_015691.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WWC3 | NM_015691.5 | c.1241A>G | p.Gln414Arg | missense_variant | 10/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WWC3 | ENST00000380861.10 | c.1241A>G | p.Gln414Arg | missense_variant | 10/24 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000180 AC: 2AN: 111272Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33482
GnomAD3 exomes AF: 0.0000221 AC: 4AN: 180703Hom.: 0 AF XY: 0.0000449 AC XY: 3AN XY: 66809
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1097441Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 1AN XY: 363241
GnomAD4 genome ? AF: 0.0000180 AC: 2AN: 111327Hom.: 0 Cov.: 23 AF XY: 0.0000298 AC XY: 1AN XY: 33547
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.869A>G (p.Q290R) alteration is located in exon 9 (coding exon 8) of the WWC3 gene. This alteration results from a A to G substitution at nucleotide position 869, causing the glutamine (Q) at amino acid position 290 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