11-88294006-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_ModerateBP6_ModerateBP7BS1
The NM_001814.6(CTSC):c.1392G>A(p.Ter464Ter) variant causes a stop retained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,613,884 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 Likely benign (★).
Frequency
Consequence
NM_001814.6 stop_retained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152082Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000718 AC: 18AN: 250864Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135550
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461684Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727154
GnomAD4 genome AF: 0.000217 AC: 33AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74424
ClinVar
Submissions by phenotype
Papillon-Lefèvre syndrome;C1855627:Haim-Munk syndrome;C4551681:Periodontitis, aggressive 1 Benign:1
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CTSC-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at