rs754663076
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001323289.2(CDKL5):c.1038C>T(p.Ile346=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000912 in 1,096,707 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001323289.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKL5 | NM_001323289.2 | c.1038C>T | p.Ile346= | synonymous_variant | 12/18 | ENST00000623535.2 | |
CDKL5 | NM_001037343.2 | c.1038C>T | p.Ile346= | synonymous_variant | 13/22 | ||
CDKL5 | NM_003159.3 | c.1038C>T | p.Ile346= | synonymous_variant | 12/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKL5 | ENST00000623535.2 | c.1038C>T | p.Ile346= | synonymous_variant | 12/18 | 1 | NM_001323289.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183409Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67853
GnomAD4 exome AF: 9.12e-7 AC: 1AN: 1096707Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 1AN XY: 362091
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 2;CN128785:Angelman syndrome-like Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 07, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at