X-41542687-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001367721.1(CASK):c.2155+4G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000701 in 1,140,780 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. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001367721.1 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CASK | NM_001367721.1 | c.2155+4G>A | splice_region_variant, intron_variant | Intron 22 of 26 | ENST00000378163.7 | NP_001354650.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000895 AC: 1AN: 111765Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33931
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 182524Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67026
GnomAD4 exome AF: 0.00000680 AC: 7AN: 1029015Hom.: 0 Cov.: 22 AF XY: 0.00000639 AC XY: 2AN XY: 312753
GnomAD4 genome AF: 0.00000895 AC: 1AN: 111765Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33931
ClinVar
Submissions by phenotype
CASK-related disorder Uncertain:1
The CASK c.2155+4G>A variant is a splice region variant. A literature search was performed for the gene and cDNA change. No publications were found based on this search. This variant is reported at a frequency of 0.000037 in the European (non-Finnish) population of the Genome Aggregation Database (version 2.1.1). Based on the available evidence, the c.2155+4G>A variant is classified as a variant of uncertain significance for CASK-related disorders. -
Intellectual disability, CASK-related, X-linked Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at