rs41267497

chr1-201043469-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000069.3(CACNA1S):c.4860C>T(p.Pro1620=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,613,800 control chromosomes in the GnomAD database, including 18,382 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1166 hom., cov: 31)

Exomes 𝑓: 0.14 ( 17216 hom. )

Consequence

CACNA1S
NM_000069.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:12

Conservation

PhyloP100: -1.20

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 1-201043469-G-A is Benign according to our data. Variant chr1-201043469-G-A is described in ClinVar as [Benign]. Clinvar id is 254841.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-201043469-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-1.2 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 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.4860C>T	p.Pro1620=	synonymous_variant	40/44	ENST00000362061.4
CACNA1S	XM_005245478.4 linkuse as main transcript	c.4803C>T	p.Pro1601=	synonymous_variant	39/43

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNA1S	ENST00000362061.4 linkuse as main transcript	c.4860C>T	p.Pro1620=	synonymous_variant	40/44	1	NM_000069.3	P2

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15883

AN:

151930

Hom.:

1167

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0296

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.0901

Gnomad ASJ

AF:

0.105

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.0218

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.110

GnomAD3 exomes

AF:

0.105

AC:

26402

AN:

251320

Hom.:

1917

AF XY:

0.105

AC XY:

14250

AN XY:

135842

show subpopulations

Gnomad AFR exome

AF:

0.0262

Gnomad AMR exome

AF:

0.0672

Gnomad ASJ exome

AF:

0.105

Gnomad EAS exome

AF:

0.000435

Gnomad SAS exome

AF:

0.0264

Gnomad FIN exome

AF:

0.127

Gnomad NFE exome

AF:

0.161

Gnomad OTH exome

AF:

0.114

GnomAD4 exome

AF:

0.144

AC:

210454

AN:

1461752

Hom.:

17216

Cov.:

AF XY:

0.140

AC XY:

102151

AN XY:

727178

show subpopulations

Gnomad4 AFR exome

AF:

0.0234

Gnomad4 AMR exome

AF:

0.0697

Gnomad4 ASJ exome

AF:

0.107

Gnomad4 EAS exome

AF:

0.000277

Gnomad4 SAS exome

AF:

0.0267

Gnomad4 FIN exome

AF:

0.131

Gnomad4 NFE exome

AF:

0.168

Gnomad4 OTH exome

AF:

0.120

GnomAD4 genome

AF:

0.104

AC:

15880

AN:

152048

Hom.:

1166

Cov.:

AF XY:

0.101

AC XY:

7472

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.0296

Gnomad4 AMR

AF:

0.0899

Gnomad4 ASJ

AF:

0.105

Gnomad4 EAS

AF:

0.000388

Gnomad4 SAS

AF:

0.0220

Gnomad4 FIN

AF:

0.125

Gnomad4 NFE

AF:

0.162

Gnomad4 OTH

AF:

0.109

Alfa

AF:

0.135

Hom.:

686

Bravo

AF:

0.101

Asia WGS

AF:

0.0170

AC:

AN:

3478

EpiCase

AF:

0.153

EpiControl

AF:

0.161

ClinVar

Significance: Benign

Submissions summary: Benign:12

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

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, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 28, 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 28, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Apr 11, 2023	- -
Benign, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Feb 05, 2024	- -

Hypokalemic periodic paralysis, type 1

Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 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	- -

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

-0.87

Cadd

Benign

0.17

Dann

Benign

0.40

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