X-18564526-GATATATATATAT-GATATATAT
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS1
The NM_001323289.2(CDKL5):c.145+25_145+28del variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0039 in 594,491 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001323289.2 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDKL5 | NM_001323289.2 | c.145+25_145+28del | splice_donor_5th_base_variant, intron_variant | ENST00000623535.2 | NP_001310218.1 | |||
CDKL5 | NM_001037343.2 | c.145+25_145+28del | splice_donor_5th_base_variant, intron_variant | NP_001032420.1 | ||||
CDKL5 | NM_003159.3 | c.145+25_145+28del | splice_donor_5th_base_variant, intron_variant | NP_003150.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDKL5 | ENST00000623535.2 | c.145+25_145+28del | splice_donor_5th_base_variant, intron_variant | 1 | NM_001323289.2 | ENSP00000485244 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000429 AC: 4AN: 93248Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0AN XY: 23402
GnomAD3 exomes AF: 0.00334 AC: 243AN: 72668Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 10808
GnomAD4 exome AF: 0.00462 AC: 2317AN: 501268Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 120376
GnomAD4 genome AF: 0.0000429 AC: 4AN: 93223Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0AN XY: 23403
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 2;CN128785:Angelman syndrome-like Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at