chr2-179945259-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020943.3(CWC22):c.2597G>A(p.Ser866Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000583 in 1,613,724 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020943.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000926 AC: 23AN: 248506Hom.: 0 AF XY: 0.0000816 AC XY: 11AN XY: 134800
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461466Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 726994
GnomAD4 genome AF: 0.000289 AC: 44AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.000363 AC XY: 27AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2597G>A (p.S866N) alteration is located in exon 20 (coding exon 19) of the CWC22 gene. This alteration results from a G to A substitution at nucleotide position 2597, causing the serine (S) at amino acid position 866 to be replaced by an asparagine (N). 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