rs777490768
Variant summary
Our verdict is Uncertain significance. Variant got -1 ACMG points: 0P and 1B. BP4
This summary comes from the ClinGen Evidence Repository: The c.65-4A>G variant in CDKL5 is present in 1 XX individual in gnomAD (does not meet BS1 based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions). Splice prediction analysis, using multiple computational tools does not suggest an impact to splicing (BP4). In summary, the c.65-4A>G in CDKL5 is classified as a variant of uncertain significance based on the ACMG/AMP criteria (BP4). LINK:https://erepo.genome.network/evrepo/ui/classification/CA10360187/MONDO:0100039/034
Frequency
Consequence
NM_001323289.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKL5 | NM_001323289.2 | c.65-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000623535.2 | |||
CDKL5 | NM_001037343.2 | c.65-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
CDKL5 | NM_003159.3 | c.65-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKL5 | ENST00000623535.2 | c.65-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001323289.2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.00000547 AC: 1AN: 182920Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67452
GnomAD4 exome AF: 9.28e-7 AC: 1AN: 1077342Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 346350
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 14, 2016 | - - |
CDKL5 disorder Uncertain:1
Uncertain significance, reviewed by expert panel | curation | ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel | Oct 13, 2023 | The c.65-4A>G variant in CDKL5 is present in 1 XX individual in gnomAD (does not meet BS1 based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions). Splice prediction analysis, using multiple computational tools does not suggest an impact to splicing (BP4). In summary, the c.65-4A>G in CDKL5 is classified as a variant of uncertain significance based on the ACMG/AMP criteria (BP4). - |
Developmental and epileptic encephalopathy, 2;CN128785:Angelman syndrome-like Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 09, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at