chrX-41531085-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001367721.1(CASK):c.2442G>A(p.Ala814=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00106 in 1,209,563 control chromosomes in the GnomAD database, including 13 homozygotes. There are 700 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A814A) has been classified as Likely benign.
Frequency
Consequence
NM_001367721.1 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASK | NM_001367721.1 | c.2442G>A | p.Ala814= | synonymous_variant | 25/27 | ENST00000378163.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASK | ENST00000378163.7 | c.2442G>A | p.Ala814= | synonymous_variant | 25/27 | 5 | NM_001367721.1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000527 AC: 59AN: 112007Hom.: 0 Cov.: 23 AF XY: 0.000790 AC XY: 27AN XY: 34171
GnomAD3 exomes AF: 0.00193 AC: 355AN: 183505Hom.: 3 AF XY: 0.00300 AC XY: 204AN XY: 67937
GnomAD4 exome AF: 0.00111 AC: 1223AN: 1097506Hom.: 13 Cov.: 31 AF XY: 0.00185 AC XY: 673AN XY: 362864
GnomAD4 genome AF: 0.000527 AC: 59AN: 112057Hom.: 0 Cov.: 23 AF XY: 0.000789 AC XY: 27AN XY: 34231
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 11, 2017 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 19, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 01, 2018 | - - |
CASK-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 11, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Intellectual disability, CASK-related, X-linked Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at