Variant 11-118133748-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_174934.4(SCN4B):c.*3279G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00314 in 454,530 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0038 ( 12 hom. )

Consequence

SCN4B
NM_174934.4 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.47

Variant links:

Genes affected

SCN4B (HGNC:10592): (sodium voltage-gated channel beta subunit 4) The protein encoded by this gene is one of several sodium channel beta subunits. These subunits interact with voltage-gated alpha subunits to change sodium channel kinetics. The encoded transmembrane protein forms interchain disulfide bonds with SCN2A. Defects in this gene are a cause of long QT syndrome type 10 (LQT10). Three protein-coding and one non-coding transcript variant have been found for this gene.[provided by RefSeq, Mar 2009]

SCN4B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 11-118133748-C-T is Benign according to our data. Variant chr11-118133748-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 302584.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 275 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
SCN4B	NM_174934.4 linkuse as main transcript	c.*3279G>A	3_prime_UTR_variant	5/5	ENST00000324727.9	NP_777594.1
SCN4B	NM_001142348.2 linkuse as main transcript	c.*3279G>A	3_prime_UTR_variant	3/3		NP_001135820.1
SCN4B	NM_001142349.2 linkuse as main transcript	c.*3279G>A	3_prime_UTR_variant	4/4		NP_001135821.1
SCN4B	NR_024527.2 linkuse as main transcript	n.3955G>A	non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCN4B	ENST00000324727.9 linkuse as main transcript	c.*3279G>A	3_prime_UTR_variant	5/5	1	NM_174934.4	ENSP00000322460	P1	Q8IWT1-1
SCN4B	ENST00000415030.6 linkuse as main transcript	n.4109G>A	non_coding_transcript_exon_variant	4/4	1
SCN4B	ENST00000423160.2 linkuse as main transcript	n.3600G>A	non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes

AF:

0.00181

AC:

276

AN:

152184

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000410

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00183

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00931

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00248

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00320

AC:

437

AN:

136674

Hom.:

AF XY:

0.00368

AC XY:

273

AN XY:

74198

show subpopulations

Gnomad AFR exome

AF:

0.000622

Gnomad AMR exome

AF:

0.00184

Gnomad ASJ exome

AF:

0.00229

Gnomad EAS exome

AF:

0.0000952

Gnomad SAS exome

AF:

0.00965

Gnomad FIN exome

AF:

0.000371

Gnomad NFE exome

AF:

0.00246

Gnomad OTH exome

AF:

0.00337

GnomAD4 exome

AF:

0.00382

AC:

1154

AN:

302228

Hom.:

Cov.:

AF XY:

0.00447

AC XY:

770

AN XY:

172258

show subpopulations

Gnomad4 AFR exome

AF:

0.000818

Gnomad4 AMR exome

AF:

0.00180

Gnomad4 ASJ exome

AF:

0.00269

Gnomad4 EAS exome

AF:

0.000109

Gnomad4 SAS exome

AF:

0.00944

Gnomad4 FIN exome

AF:

0.000782

Gnomad4 NFE exome

AF:

0.00275

Gnomad4 OTH exome

AF:

0.00370

GnomAD4 genome

AF:

0.00181

AC:

275

AN:

152302

Hom.:

Cov.:

AF XY:

0.00203

AC XY:

151

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.000409

Gnomad4 AMR

AF:

0.00183

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00911

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00248

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.00220

Hom.:

Bravo

AF:

0.00176

Asia WGS

AF:

0.00260

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Congenital long QT syndrome

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

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.62

DANN

Benign

0.83

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