rs375004542
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001367721.1(CASK):c.1315-10A>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000783 in 1,149,955 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 34 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001367721.1 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASK | NM_001367721.1 | c.1315-10A>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000378163.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASK | ENST00000378163.7 | c.1315-10A>G | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001367721.1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000894 AC: 10AN: 111798Hom.: 0 Cov.: 22 AF XY: 0.0000294 AC XY: 1AN XY: 33972
GnomAD3 exomes AF: 0.0000856 AC: 15AN: 175280Hom.: 0 AF XY: 0.000116 AC XY: 7AN XY: 60360
GnomAD4 exome AF: 0.0000771 AC: 80AN: 1038101Hom.: 0 Cov.: 24 AF XY: 0.000106 AC XY: 33AN XY: 310129
GnomAD4 genome ? AF: 0.0000894 AC: 10AN: 111854Hom.: 0 Cov.: 22 AF XY: 0.0000294 AC XY: 1AN XY: 34038
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 27, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 28, 2019 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 13, 2016 | - - |
Intellectual disability, CASK-related, X-linked Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at