rs2297902

chr1-201065943-G-Achr1-201065943-G-C

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_000069.3(CACNA1S):c.2748C>T(p.His916=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0199 in 1,608,184 control chromosomes in the GnomAD database, including 1,214 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.023 ( 172 hom., cov: 32)

Exomes 𝑓: 0.020 ( 1042 hom. )

Consequence

CACNA1S
NM_000069.3 splice_region, synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:13

Conservation

PhyloP100: 0.533

Variant links:

Genes affected

CACNA1S (HGNC:1397): (calcium voltage-gated channel subunit alpha1 S) This gene encodes one of the five subunits of the slowly inactivating L-type voltage-dependent calcium channel in skeletal muscle cells. Mutations in this gene have been associated with hypokalemic periodic paralysis, thyrotoxic periodic paralysis and malignant hyperthermia susceptibility. [provided by RefSeq, Jul 2008]

CACNA1S links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BP6

Variant 1-201065943-G-A is Benign according to our data. Variant chr1-201065943-G-A is described in ClinVar as [Benign]. Clinvar id is 254822.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-201065943-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.533 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNA1S	NM_000069.3 linkuse as main transcript	c.2748C>T	p.His916=	splice_region_variant, synonymous_variant	22/44	ENST00000362061.4
CACNA1S	XM_005245478.4 linkuse as main transcript	c.2748C>T	p.His916=	splice_region_variant, synonymous_variant	22/43

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNA1S	ENST00000362061.4 linkuse as main transcript	c.2748C>T	p.His916=	splice_region_variant, synonymous_variant	22/44	1	NM_000069.3	P2

Frequencies

GnomAD3 genomes

AF:

0.0230

AC:

3496

AN:

152172

Hom.:

162

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0109

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0352

Gnomad ASJ

AF:

0.0193

Gnomad EAS

AF:

0.202

Gnomad SAS

AF:

0.0319

Gnomad FIN

AF:

0.0367

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0113

Gnomad OTH

AF:

0.0320

GnomAD3 exomes

AF:

0.0383

AC:

9443

AN:

246738

Hom.:

459

AF XY:

0.0362

AC XY:

4831

AN XY:

133418

show subpopulations

Gnomad AFR exome

AF:

0.0114

Gnomad AMR exome

AF:

0.0644

Gnomad ASJ exome

AF:

0.0195

Gnomad EAS exome

AF:

0.199

Gnomad SAS exome

AF:

0.0346

Gnomad FIN exome

AF:

0.0349

Gnomad NFE exome

AF:

0.0117

Gnomad OTH exome

AF:

0.0308

GnomAD4 exome

AF:

0.0196

AC:

28527

AN:

1455894

Hom.:

1042

Cov.:

AF XY:

0.0199

AC XY:

14400

AN XY:

724474

show subpopulations

Gnomad4 AFR exome

AF:

0.0109

Gnomad4 AMR exome

AF:

0.0620

Gnomad4 ASJ exome

AF:

0.0207

Gnomad4 EAS exome

AF:

0.194

Gnomad4 SAS exome

AF:

0.0349

Gnomad4 FIN exome

AF:

0.0360

Gnomad4 NFE exome

AF:

0.00951

Gnomad4 OTH exome

AF:

0.0256

GnomAD4 genome

AF:

0.0232

AC:

3526

AN:

152290

Hom.:

172

Cov.:

AF XY:

0.0254

AC XY:

1889

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0110

Gnomad4 AMR

AF:

0.0351

Gnomad4 ASJ

AF:

0.0193

Gnomad4 EAS

AF:

0.202

Gnomad4 SAS

AF:

0.0321

Gnomad4 FIN

AF:

0.0367

Gnomad4 NFE

AF:

0.0113

Gnomad4 OTH

AF:

0.0421

Alfa

AF:

0.0142

Hom.:

Bravo

AF:

0.0255

Asia WGS

AF:

0.116

AC:

403

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:13

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 18, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Malignant hyperthermia, susceptibility to, 5

Benign:3

Benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 05, 2018	- -
Benign, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Feb 05, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Apr 11, 2023	- -

Hypokalemic periodic paralysis, type 1

Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Mar 06, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Apr 11, 2023	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 27, 2018	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -

Congenital myopathy 18

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Thyrotoxic periodic paralysis, susceptibility to, 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Malignant hyperthermia, susceptibility to, 5;C3714580:Hypokalemic periodic paralysis, type 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

Cadd

Benign

Dann

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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