1-196228225-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_198503.5(KCNT2):c.3407G>A(p.Ter1136Ter) variant causes a stop retained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000126 in 1,585,534 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 (no stars).
Frequency
Consequence
NM_198503.5 stop_retained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000654 AC: 16AN: 244576Hom.: 0 AF XY: 0.0000756 AC XY: 10AN XY: 132210
GnomAD4 exome AF: 0.0000126 AC: 18AN: 1433472Hom.: 0 Cov.: 25 AF XY: 0.0000140 AC XY: 10AN XY: 714350
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74274
ClinVar
Submissions by phenotype
KCNT2-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