rs368344738
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000379989.6(CDKL5):c.2841G>A(p.Pro947=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000413 in 1,210,173 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000379989.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RS1 | NM_000330.4 | c.185-3121C>T | intron_variant | ENST00000379984.4 | |||
CDKL5 | NM_001037343.2 | c.2841G>A | p.Pro947= | synonymous_variant | 21/22 | ||
CDKL5 | NM_003159.3 | c.2841G>A | p.Pro947= | synonymous_variant | 20/21 | ||
RS1 | XM_047442337.1 | c.-70C>T | 5_prime_UTR_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RS1 | ENST00000379984.4 | c.185-3121C>T | intron_variant | 1 | NM_000330.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000892 AC: 1AN: 112069Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34241
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183499Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67931
GnomAD4 exome AF: 0.00000364 AC: 4AN: 1098104Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 363458
GnomAD4 genome ? AF: 0.00000892 AC: 1AN: 112069Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34241
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 2;CN128785:Angelman syndrome-like Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 30, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at