NM_001232.4:c.784-17T>A
Variant names:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001232.4(CASQ2):c.784-17T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 1,569,936 control chromosomes in the GnomAD database, including 252,790 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.60 ( 27671 hom., cov: 33)
Exomes 𝑓: 0.56 ( 225119 hom. )
Consequence
CASQ2
NM_001232.4 intron
NM_001232.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.349
Genes affected
CASQ2 (HGNC:1513): (calsequestrin 2) The protein encoded by this gene specifies the cardiac muscle family member of the calsequestrin family. Calsequestrin is localized to the sarcoplasmic reticulum in cardiac and slow skeletal muscle cells. The protein is a calcium binding protein that stores calcium for muscle function. Mutations in this gene cause stress-induced polymorphic ventricular tachycardia, also referred to as catecholaminergic polymorphic ventricular tachycardia 2 (CPVT2), a disease characterized by bidirectional ventricular tachycardia that may lead to cardiac arrest. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 1-115717911-A-T is Benign according to our data. Variant chr1-115717911-A-T is described in ClinVar as [Benign]. Clinvar id is 257652.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-115717911-A-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.599 AC: 90944AN: 151924Hom.: 27632 Cov.: 33
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GnomAD3 exomes AF: 0.580 AC: 145689AN: 251066Hom.: 42672 AF XY: 0.575 AC XY: 78076AN XY: 135676
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GnomAD4 exome AF: 0.562 AC: 796475AN: 1417894Hom.: 225119 Cov.: 26 AF XY: 0.561 AC XY: 397419AN XY: 708204
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GnomAD4 genome AF: 0.599 AC: 91037AN: 152042Hom.: 27671 Cov.: 33 AF XY: 0.601 AC XY: 44686AN XY: 74312
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ClinVar
Significance: Benign
Submissions summary: Benign:10
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Catecholaminergic polymorphic ventricular tachycardia 2 Benign:4
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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
- -
Sep 21, 2015
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Oct 09, 2014
Genome Diagnostics Laboratory, University Medical Center Utrecht
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Jul 14, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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not specified Benign:2
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PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
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Clinical Genetics, Academic Medical Center
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
- -
not provided Benign:2
Mar 03, 2015
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
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Catecholaminergic polymorphic ventricular tachycardia Benign:1
Sep 23, 2022
Cohesion Phenomics
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
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Catecholaminergic polymorphic ventricular tachycardia 1 Benign:1
Feb 04, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at