X-18613214-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001323289.2(CDKL5):c.2215C>T(p.Leu739=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000753 in 1,195,657 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L739L) has been classified as Likely benign.
Frequency
Consequence
NM_001323289.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKL5 | NM_001323289.2 | c.2215C>T | p.Leu739= | synonymous_variant | 15/18 | ENST00000623535.2 | |
CDKL5 | NM_001037343.2 | c.2215C>T | p.Leu739= | synonymous_variant | 16/22 | ||
CDKL5 | NM_003159.3 | c.2215C>T | p.Leu739= | synonymous_variant | 15/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKL5 | ENST00000623535.2 | c.2215C>T | p.Leu739= | synonymous_variant | 15/18 | 1 | NM_001323289.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000904 AC: 1AN: 110629Hom.: 0 Cov.: 22 AF XY: 0.0000304 AC XY: 1AN XY: 32893
GnomAD3 exomes AF: 0.0000273 AC: 5AN: 183443Hom.: 0 AF XY: 0.0000737 AC XY: 5AN XY: 67879
GnomAD4 exome AF: 0.00000737 AC: 8AN: 1084991Hom.: 0 Cov.: 29 AF XY: 0.0000170 AC XY: 6AN XY: 352223
GnomAD4 genome AF: 0.00000904 AC: 1AN: 110666Hom.: 0 Cov.: 22 AF XY: 0.0000304 AC XY: 1AN XY: 32940
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 26, 2015 | - - |
Developmental and epileptic encephalopathy, 2;CN128785:Angelman syndrome-like Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at