rs56889721

chr1-115725557-GAAAAAAAAAAAAAAA-Gchr1-115725557-GAAAAAAAAAAAAAAA-GAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAchr1-115725557-GAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001232.4(CASQ2):c.738-19_738-5del variant causes a splice region, splice polypyrimidine tract, intron change. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 0)
• Consequence: CASQ2 NM_001232.4 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 6.12

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]

ACMG classification

Verdict is Likely_benign. Variant got -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 id is 2912893.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASQ2	NM_001232.4	c.738-19_738-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000261448.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASQ2	ENST00000261448.6	c.738-19_738-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_001232.4	P1
CASQ2	ENST00000488931.2	c.*110-19_*110-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant		3

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

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Catecholaminergic polymorphic ventricular tachycardia 1 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Mar 09, 2023

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56889721; hg19: chr1-116268178;