X-18564526-GATATATATATAT-GATATATATAT
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The ENST00000623535.2(CDKL5):c.145+5_145+6delAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0538 in 556,775 control chromosomes in the GnomAD database, including 12 homozygotes. There are 400 hemizygotes in GnomAD. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000623535.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDKL5 | NM_001323289.2 | c.145+27_145+28delAT | intron_variant | Intron 4 of 17 | ENST00000623535.2 | NP_001310218.1 | ||
CDKL5 | NM_001037343.2 | c.145+27_145+28delAT | intron_variant | Intron 5 of 21 | NP_001032420.1 | |||
CDKL5 | NM_003159.3 | c.145+27_145+28delAT | intron_variant | Intron 4 of 20 | NP_003150.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0105 AC: 977AN: 93107Hom.: 5 Cov.: 19 AF XY: 0.00870 AC XY: 203AN XY: 23339
GnomAD3 exomes AF: 0.0643 AC: 4674AN: 72668Hom.: 0 AF XY: 0.000648 AC XY: 7AN XY: 10808
GnomAD4 exome AF: 0.0625 AC: 29001AN: 463698Hom.: 7 AF XY: 0.00206 AC XY: 197AN XY: 95852
GnomAD4 genome AF: 0.0105 AC: 977AN: 93077Hom.: 5 Cov.: 19 AF XY: 0.00870 AC XY: 203AN XY: 23337
ClinVar
Submissions by phenotype
not provided Benign:1
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Developmental and epileptic encephalopathy, 2;CN128785:Angelman syndrome-like Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at