chrX-18425834-C-CTT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001323289.2(CDKL5):c.-163+139_-163+140insTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00314 in 112,888 control chromosomes in the GnomAD database, including 1 homozygotes. There are 130 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0031 ( 1 hom., 130 hem., cov: 24)
Consequence
CDKL5
NM_001323289.2 intron
NM_001323289.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.296
Genes affected
CDKL5 (HGNC:11411): (cyclin dependent kinase like 5) This gene is a member of Ser/Thr protein kinase family and encodes a phosphorylated protein with protein kinase activity. Mutations in this gene have been associated with X-linked infantile spasm syndrome (ISSX), also known as X-linked West syndrome, and Rett syndrome (RTT). Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant X-18425834-C-CTT is Benign according to our data. Variant chrX-18425834-C-CTT is described in ClinVar as [Likely_benign]. Clinvar id is 1194507.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00314 (354/112888) while in subpopulation NFE AF= 0.00393 (209/53134). AF 95% confidence interval is 0.0035. There are 1 homozygotes in gnomad4. There are 130 alleles in male gnomad4 subpopulation. Median coverage is 24. This position pass quality control queck.
BS2
?
High Hemizygotes in GnomAd at 130 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKL5 | NM_001323289.2 | c.-163+139_-163+140insTT | intron_variant | ENST00000623535.2 | |||
CDKL5 | NM_003159.3 | c.-163+139_-163+140insTT | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKL5 | ENST00000623535.2 | c.-163+139_-163+140insTT | intron_variant | 1 | NM_001323289.2 | P1 | |||
CDKL5 | ENST00000379996.7 | c.-163+139_-163+140insTT | intron_variant | 1 | |||||
CDKL5 | ENST00000674046.1 | c.-163+139_-163+140insTT | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00314 AC: 354AN: 112840Hom.: 1 Cov.: 24 AF XY: 0.00371 AC XY: 130AN XY: 35014
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GnomAD4 genome ? AF: 0.00314 AC: 354AN: 112888Hom.: 1 Cov.: 24 AF XY: 0.00371 AC XY: 130AN XY: 35072
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 20, 2019 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at