chrX-41559852-AG-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001367721.1(CASK):c.1669-6del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,196,977 control chromosomes in the GnomAD database, including 1 homozygotes. There are 7 hemizygotes in GnomAD. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001367721.1 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASK | NM_001367721.1 | c.1669-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000378163.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASK | ENST00000378163.7 | c.1669-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001367721.1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112131Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34319
GnomAD4 exome AF: 0.0000249 AC: 27AN: 1084846Hom.: 1 Cov.: 27 AF XY: 0.0000171 AC XY: 6AN XY: 351088
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112131Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34319
ClinVar
Submissions by phenotype
Intellectual disability, CASK-related, X-linked Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 30, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at