11-2885400-G-T
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_001122630.2(CDKN1C):c.57C>A(p.Cys19*) variant causes a stop gained change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_001122630.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1405962Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 695270
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Beckwith-Wiedemann syndrome Pathogenic:2
PM2_Supporting+PVS1 -
This variant has not been reported in the literature in individuals with CDKN1C-related conditions. This sequence change creates a premature translational stop signal (p.Cys30*) in the CDKN1C gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CDKN1C are known to be pathogenic (PMID: 20503313). This variant is not present in population databases (ExAC no frequency). For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.