rs765011302
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001323289.2(CDKL5):āc.1692T>Cā(p.His564=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,210,426 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001323289.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKL5 | NM_001323289.2 | c.1692T>C | p.His564= | synonymous_variant | 12/18 | ENST00000623535.2 | |
CDKL5 | NM_001037343.2 | c.1692T>C | p.His564= | synonymous_variant | 13/22 | ||
CDKL5 | NM_003159.3 | c.1692T>C | p.His564= | synonymous_variant | 12/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKL5 | ENST00000623535.2 | c.1692T>C | p.His564= | synonymous_variant | 12/18 | 1 | NM_001323289.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000891 AC: 1AN: 112203Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34357
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183286Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67786
GnomAD4 exome AF: 0.0000537 AC: 59AN: 1098223Hom.: 0 Cov.: 32 AF XY: 0.0000413 AC XY: 15AN XY: 363577
GnomAD4 genome ? AF: 0.00000891 AC: 1AN: 112203Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34357
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 22, 2019 | - - |
CDKL5-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 14, 2019 | 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). - |
Developmental and epileptic encephalopathy, 2;CN128785:Angelman syndrome-like Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 31, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at