chr11-17779604-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001112741.2(KCNC1):c.1653C>T(p.Thr551Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000406 in 1,550,902 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 (★★). Synonymous variant affecting the same amino acid position (i.e. T551T) has been classified as Likely benign.
Frequency
Consequence
NM_001112741.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000522 AC: 8AN: 153390Hom.: 0 AF XY: 0.0000369 AC XY: 3AN XY: 81406
GnomAD4 exome AF: 0.0000357 AC: 50AN: 1398724Hom.: 0 Cov.: 31 AF XY: 0.0000333 AC XY: 23AN XY: 689896
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74332
ClinVar
Submissions by phenotype
Progressive myoclonic epilepsy type 7 Benign:1
- -
not provided Benign:1
KCNC1: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at