X-18579749-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001323289.2(CDKL5):c.283-99C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 781,995 control chromosomes in the GnomAD database, including 28,867 homozygotes. There are 71,175 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001323289.2 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDKL5 | NM_001323289.2 | c.283-99C>A | intron_variant | Intron 5 of 17 | ENST00000623535.2 | NP_001310218.1 | ||
CDKL5 | NM_001037343.2 | c.283-99C>A | intron_variant | Intron 6 of 21 | NP_001032420.1 | |||
CDKL5 | NM_003159.3 | c.283-99C>A | intron_variant | Intron 5 of 20 | NP_003150.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.283 AC: 31182AN: 110051Hom.: 3437 Cov.: 23 AF XY: 0.285 AC XY: 9237AN XY: 32391
GnomAD4 exome AF: 0.319 AC: 214153AN: 671895Hom.: 25434 AF XY: 0.337 AC XY: 61924AN XY: 183723
GnomAD4 genome AF: 0.283 AC: 31182AN: 110100Hom.: 3433 Cov.: 23 AF XY: 0.285 AC XY: 9251AN XY: 32450
ClinVar
Submissions by phenotype
not provided Benign:2Other:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
- -
- -
not specified Benign:1
Common SNP -
CDKL5 disorder Benign:1
This variant has been collected from RettBASE and curated to current modified ACMG/AMP criteria. Based on the classification scheme defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders Specifications to the ACMG/AMP Variant Interpretation Guidelines VCEP 3.0, this variant is classified as benign. At least the following criteria are met: The allele frequency of this variant in at least one population in gnomAD v4 is higher than the 0.03% threshold defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders VCEP 3.0 (BA1). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at