11-17771748-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BP7
The NM_001112741.2(KCNC1):c.654C>A(p.Ile218=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,874 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 (★). Synonymous variant affecting the same amino acid position (i.e. I218I) has been classified as Likely benign.
Frequency
Consequence
NM_001112741.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNC1 | NM_001112741.2 | c.654C>A | p.Ile218= | synonymous_variant | 2/4 | ENST00000265969.8 | |
KCNC1 | NM_004976.4 | c.654C>A | p.Ile218= | synonymous_variant | 2/2 | ||
KCNC1 | XM_047426916.1 | c.654C>A | p.Ile218= | synonymous_variant | 2/4 | ||
KCNC1 | XR_930866.3 | n.1876C>A | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNC1 | ENST00000265969.8 | c.654C>A | p.Ile218= | synonymous_variant | 2/4 | 5 | NM_001112741.2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251486Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135920
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727234
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Progressive myoclonic epilepsy type 7 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 09, 2022 | 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 542108). This sequence change affects codon 218 of the KCNC1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the KCNC1 protein. This variant is present in population databases (rs747207268, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with KCNC1-related conditions. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at