rs267608394
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000379989.6(CDKL5):c.*15C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000414 in 1,206,540 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000379989.6 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RS1 | NM_000330.4 | c.184+3094G>T | intron_variant | ENST00000379984.4 | |||
CDKL5 | NM_001037343.2 | c.*15C>A | 3_prime_UTR_variant | 22/22 | |||
CDKL5 | NM_003159.3 | c.*15C>A | 3_prime_UTR_variant | 21/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKL5 | ENST00000379989.6 | c.*15C>A | 3_prime_UTR_variant | 22/22 | 1 | ||||
CDKL5 | ENST00000379996.7 | c.*15C>A | 3_prime_UTR_variant | 21/21 | 1 | ||||
RS1 | ENST00000379984.4 | c.184+3094G>T | intron_variant | 1 | NM_000330.4 | P1 | |||
CDKL5 | ENST00000673617.1 | downstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000888 AC: 1AN: 112594Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34740
GnomAD3 exomes AF: 0.0000114 AC: 2AN: 175751Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 60999
GnomAD4 exome AF: 0.00000366 AC: 4AN: 1093946Hom.: 0 Cov.: 30 AF XY: 0.00000556 AC XY: 2AN XY: 359544
GnomAD4 genome ? AF: 0.00000888 AC: 1AN: 112594Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34740
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at