Variant 17-63939367-C-CACACATATAT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_000334.4(SCN4A):c.*1394_*1403dupATATATGTGT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.43 ( 15906 hom., cov: 0)

Exomes 𝑓: 0.13 ( 2 hom. )

Consequence

SCN4A
NM_000334.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.130

Variant links:

Genes affected

SCN4A (HGNC:10591): (sodium voltage-gated channel alpha subunit 4) Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family. It is expressed in skeletal muscle, and mutations in this gene have been linked to several myotonia and periodic paralysis disorders. [provided by RefSeq, Jul 2008]

SCN4A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 17-63939367-C-CACACATATAT is Benign according to our data. Variant chr17-63939367-C-CACACATATAT is described in ClinVar as [Benign]. Clinvar id is 324479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCN4A	NM_000334.4 link	c.1394_1403dupATATATGTGT		3_prime_UTR_variant	24/24	ENST00000435607.3	NP_000325.4	P35499

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCN4A	ENST00000435607.3 link	c.1394_1403dupATATATGTGT		3_prime_UTR_variant	24/24	1	NM_000334.4	ENSP00000396320.1		P35499

Frequencies

GnomAD3 genomes

AF:

0.431

AC:

65261

AN:

151246

Hom.:

15902

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.602

Gnomad AMR

AF:

0.440

Gnomad ASJ

AF:

0.557

Gnomad EAS

AF:

0.456

Gnomad SAS

AF:

0.385

Gnomad FIN

AF:

0.523

Gnomad MID

AF:

0.567

Gnomad NFE

AF:

0.553

Gnomad OTH

AF:

0.474

GnomAD4 exome

AF:

0.132

AC:

AN:

Hom.:

Cov.:

AF XY:

0.113

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.148

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.431

AC:

65289

AN:

151362

Hom.:

15906

Cov.:

AF XY:

0.429

AC XY:

31701

AN XY:

73896

show subpopulations

Gnomad4 AFR

AF:

0.192

Gnomad4 AMR

AF:

0.440

Gnomad4 ASJ

AF:

0.557

Gnomad4 EAS

AF:

0.456

Gnomad4 SAS

AF:

0.385

Gnomad4 FIN

AF:

0.523

Gnomad4 NFE

AF:

0.553

Gnomad4 OTH

AF:

0.476

Asia WGS

AF:

0.400

AC:

1395

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hypokalemic periodic paralysis

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Paramyotonia congenita of Von Eulenburg

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Hyperkalemic periodic paralysis

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Congenital Myasthenic Syndrome, Recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

- -

Potassium-aggravated myotonia

Benign:1

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

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