GeneBe

rs56889721

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001232.4(CASQ2):​c.738-19_738-5delTTTTTTTTTTTTTTT variant causes a splice region, intron change. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 0)

Consequence

CASQ2
NM_001232.4 splice_region, intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.12

Publications

3 publications found
Variant links:
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 tachycardia
    Inheritance: AD, AR Classification: DEFINITIVE, MODERATE, SUPPORTIVE Submitted by: ClinGen, Orphanet
  • catecholaminergic polymorphic ventricular tachycardia 2
    Inheritance: AR, AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp, G2P
  • hypertrophic cardiomyopathy
    Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP6
Variant 1-115725557-GAAAAAAAAAAAAAAA-G is Benign according to our data. Variant chr1-115725557-GAAAAAAAAAAAAAAA-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2912893.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001232.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CASQ2
NM_001232.4
MANE Select
c.738-19_738-5delTTTTTTTTTTTTTTT
splice_region intron
N/ANP_001223.2O14958-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CASQ2
ENST00000261448.6
TSL:1 MANE Select
c.738-19_738-5delTTTTTTTTTTTTTTT
splice_region intron
N/AENSP00000261448.5O14958-1
CASQ2
ENST00000713711.1
c.879-19_879-5delTTTTTTTTTTTTTTT
splice_region intron
N/AENSP00000519014.1A0AAQ5BGS1
CASQ2
ENST00000874189.1
c.738-19_738-5delTTTTTTTTTTTTTTT
splice_region intron
N/AENSP00000544248.1

Frequencies

GnomAD3 genomes
Cov.:
0
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.00
Hom.:
284

ClinVar

ClinVar submissions as Germline
Significance:Likely benign
Revision:criteria provided, single submitter
View on ClinVar
Pathogenic
VUS
Benign
Condition
-
-
1
Catecholaminergic polymorphic ventricular tachycardia 1 (1)

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
6.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs56889721; hg19: chr1-116268178; API