11-17736104-C-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001112741.2(KCNC1):c.102C>A(p.Leu34=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000046 in 1,609,572 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. L34L) has been classified as Likely benign.
Frequency
Consequence
NM_001112741.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNC1 | NM_001112741.2 | c.102C>A | p.Leu34= | synonymous_variant | 1/4 | ENST00000265969.8 | |
KCNC1 | NM_004976.4 | c.102C>A | p.Leu34= | synonymous_variant | 1/2 | ||
KCNC1 | XM_047426916.1 | c.102C>A | p.Leu34= | synonymous_variant | 1/4 | ||
KCNC1 | XR_930866.3 | n.1324C>A | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNC1 | ENST00000265969.8 | c.102C>A | p.Leu34= | synonymous_variant | 1/4 | 5 | NM_001112741.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000209 AC: 5AN: 239788Hom.: 0 AF XY: 0.00000761 AC XY: 1AN XY: 131380
GnomAD4 exome AF: 0.0000501 AC: 73AN: 1457370Hom.: 0 Cov.: 32 AF XY: 0.0000373 AC XY: 27AN XY: 724738
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 21, 2018 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Progressive myoclonic epilepsy type 7 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at