X-18653445-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_003159.3(CDKL5):c.2994C>T(p.Phe998Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00043 in 1,209,395 control chromosomes in the GnomAD database, including 3 homozygotes. There are 124 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003159.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RS1 | NM_000330.4 | c.184+3208G>A | intron_variant | Intron 3 of 5 | ENST00000379984.4 | NP_000321.1 | ||
CDKL5 | NM_001037343.2 | c.2994C>T | p.Phe998Phe | synonymous_variant | Exon 22 of 22 | NP_001032420.1 | ||
CDKL5 | NM_003159.3 | c.2994C>T | p.Phe998Phe | synonymous_variant | Exon 21 of 21 | NP_003150.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDKL5 | ENST00000379989.6 | c.2994C>T | p.Phe998Phe | synonymous_variant | Exon 22 of 22 | 1 | ENSP00000369325.3 | |||
CDKL5 | ENST00000379996.7 | c.2994C>T | p.Phe998Phe | synonymous_variant | Exon 21 of 21 | 1 | ENSP00000369332.3 | |||
RS1 | ENST00000379984.4 | c.184+3208G>A | intron_variant | Intron 3 of 5 | 1 | NM_000330.4 | ENSP00000369320.3 | |||
CDKL5 | ENST00000673617.1 | n.266C>T | non_coding_transcript_exon_variant | Exon 3 of 3 |
Frequencies
GnomAD3 genomes AF: 0.00223 AC: 249AN: 111670Hom.: 1 Cov.: 23 AF XY: 0.00192 AC XY: 65AN XY: 33834
GnomAD3 exomes AF: 0.000577 AC: 105AN: 181879Hom.: 0 AF XY: 0.000406 AC XY: 27AN XY: 66439
GnomAD4 exome AF: 0.000247 AC: 271AN: 1097673Hom.: 2 Cov.: 31 AF XY: 0.000162 AC XY: 59AN XY: 363083
GnomAD4 genome AF: 0.00223 AC: 249AN: 111722Hom.: 1 Cov.: 23 AF XY: 0.00192 AC XY: 65AN XY: 33896
ClinVar
Submissions by phenotype
not specified Benign:2
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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 provided Benign:2
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Developmental and epileptic encephalopathy, 2 Benign:1
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History of neurodevelopmental disorder Benign:1
General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance -
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