1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAA
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001232.4(CASQ2):c.738-5delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001232.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CASQ2 | ENST00000261448.6 | c.738-5delT | splice_region_variant, intron_variant | Intron 6 of 10 | 1 | NM_001232.4 | ENSP00000261448.5 | |||
CASQ2 | ENST00000488931.2 | n.*110-5delT | splice_region_variant, intron_variant | Intron 8 of 12 | 3 | ENSP00000518226.1 |
Frequencies
GnomAD3 genomes AF: 0.0284 AC: 3233AN: 113974Hom.: 51 Cov.: 0
GnomAD4 exome AF: 0.132 AC: 164324AN: 1244766Hom.: 14 Cov.: 0 AF XY: 0.128 AC XY: 79523AN XY: 619174
GnomAD4 genome AF: 0.0284 AC: 3235AN: 113944Hom.: 51 Cov.: 0 AF XY: 0.0281 AC XY: 1486AN XY: 52850
ClinVar
Submissions by phenotype
Catecholaminergic polymorphic ventricular tachycardia 2 Benign:2
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Cardiomyopathy Benign:1
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not provided Benign:1
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CASQ2-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at