1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAA
Variant summary
Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
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
Publications
- catecholaminergic polymorphic ventricular tachycardiaInheritance: AD, AR Classification: DEFINITIVE, MODERATE, SUPPORTIVE Submitted by: Orphanet, ClinGen
- catecholaminergic polymorphic ventricular tachycardia 2Inheritance: AR, AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P, Genomics England PanelApp
- hypertrophic cardiomyopathyInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
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ACMG classification
Our verdict: Benign. The variant received -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0284 AC: 3233AN: 113974Hom.: 51 Cov.: 0 show subpopulations
GnomAD4 exome AF: 0.132 AC: 164324AN: 1244766Hom.: 14 Cov.: 0 AF XY: 0.128 AC XY: 79523AN XY: 619174 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
Age Distribution
GnomAD4 genome AF: 0.0284 AC: 3235AN: 113944Hom.: 51 Cov.: 0 AF XY: 0.0281 AC XY: 1486AN XY: 52850 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Catecholaminergic polymorphic ventricular tachycardia 2 Benign:2
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not specified Benign:1
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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