1-115725557-GAAAAAAAAAAAAAAA-GAAAAA
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_001232.4(CASQ2):c.738-14_738-5delTTTTTTTTTT variant causes a splice region, intron change. The variant allele was found at a frequency of 0.00000855 in 1,402,830 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000070 ( 0 hom. )
Consequence
CASQ2
NM_001232.4 splice_region, intron
NM_001232.4 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.12
Publications
3 publications found
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]
CASQ2 Gene-Disease associations (from GenCC):
- 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
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 3AN: 114030Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
114030
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000698 AC: 9AN: 1288830Hom.: 0 AF XY: 0.00000779 AC XY: 5AN XY: 642012 show subpopulations
GnomAD4 exome
AF:
AC:
9
AN:
1288830
Hom.:
AF XY:
AC XY:
5
AN XY:
642012
show subpopulations
African (AFR)
AF:
AC:
1
AN:
28378
American (AMR)
AF:
AC:
1
AN:
31834
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22774
East Asian (EAS)
AF:
AC:
0
AN:
36490
South Asian (SAS)
AF:
AC:
1
AN:
72756
European-Finnish (FIN)
AF:
AC:
0
AN:
37156
Middle Eastern (MID)
AF:
AC:
0
AN:
3680
European-Non Finnish (NFE)
AF:
AC:
6
AN:
1002254
Other (OTH)
AF:
AC:
0
AN:
53508
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.414
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.0000263 AC: 3AN: 114000Hom.: 0 Cov.: 0 AF XY: 0.0000189 AC XY: 1AN XY: 52882 show subpopulations
GnomAD4 genome
AF:
AC:
3
AN:
114000
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
52882
show subpopulations
African (AFR)
AF:
AC:
0
AN:
30842
American (AMR)
AF:
AC:
1
AN:
10306
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2992
East Asian (EAS)
AF:
AC:
0
AN:
3814
South Asian (SAS)
AF:
AC:
0
AN:
3260
European-Finnish (FIN)
AF:
AC:
0
AN:
3528
Middle Eastern (MID)
AF:
AC:
0
AN:
224
European-Non Finnish (NFE)
AF:
AC:
2
AN:
56720
Other (OTH)
AF:
AC:
0
AN:
1546
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.558
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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