chr11-2883979-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_001122630.2(CDKN1C):c.*5+20G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,562,174 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001122630.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151982Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000124 AC: 2AN: 161678Hom.: 0 AF XY: 0.0000226 AC XY: 2AN XY: 88486
GnomAD4 exome AF: 0.0000404 AC: 57AN: 1410192Hom.: 0 Cov.: 32 AF XY: 0.0000445 AC XY: 31AN XY: 697032
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151982Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74236
ClinVar
Submissions by phenotype
Beckwith-Wiedemann syndrome Uncertain:1
This variant occurs in a non-coding region of the CDKN1C gene. It does not change the encoded amino acid sequence of the CDKN1C protein. This variant is present in population databases (rs760540648, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with CDKN1C-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at