Variant 1-115700116-CAT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001232.4(CASQ2):c.*1123_*1124delAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,464 control chromosomes in the GnomAD database, including 4,297 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.24 ( 4286 hom., cov: 25)

Exomes 𝑓: 0.22 ( 11 hom. )

Consequence

CASQ2
NM_001232.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:3

Conservation

PhyloP100: 0.363

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-115700116-CAT-C is Benign according to our data. Variant chr1-115700116-CAT-C is described in ClinVar as [Likely_benign]. Clinvar id is 292115.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASQ2	NM_001232.4 linkuse as main transcript	c.1123_1124delAT		3_prime_UTR_variant	11/11	ENST00000261448.6	NP_001223.2	O14958-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CASQ2	ENST00000261448 linkuse as main transcript	c.1123_1124delAT	3_prime_UTR_variant	11/11	1	NM_001232.4	ENSP00000261448.5	O14958-1
CASQ2	ENST00000488931.2 linkuse as main transcript	n.1695_1696delAT	non_coding_transcript_exon_variant	13/13	3		ENSP00000518226.1
CASQ2	ENST00000488931.2 linkuse as main transcript	n.1695_1696delAT	3_prime_UTR_variant	13/13	3		ENSP00000518226.1

Frequencies

GnomAD3 genomes

AF:

0.237

AC:

35966

AN:

151918

Hom.:

4279

Cov.:

show subpopulations

Gnomad AFR

AF:

0.220

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.216

Gnomad EAS

AF:

0.165

Gnomad SAS

AF:

0.290

Gnomad FIN

AF:

0.232

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.255

GnomAD4 exome

AF:

0.222

AC:

AN:

428

Hom.:

AF XY:

0.207

AC XY:

AN XY:

256

show subpopulations

Gnomad4 FIN exome

AF:

0.220

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.237

AC:

36009

AN:

152036

Hom.:

4286

Cov.:

AF XY:

0.239

AC XY:

17742

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.221

Gnomad4 AMR

AF:

0.276

Gnomad4 ASJ

AF:

0.216

Gnomad4 EAS

AF:

0.165

Gnomad4 SAS

AF:

0.291

Gnomad4 FIN

AF:

0.232

Gnomad4 NFE

AF:

0.239

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.243

Hom.:

520

Bravo

AF:

0.239

Asia WGS

AF:

0.258

AC:

895

AN:

3476

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Catecholaminergic polymorphic ventricular tachycardia

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Caudal regression sequence

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Neural tube defect

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over