Variant 11-118134148-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_174934.4(SCN4B):c.*2879T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 454,150 control chromosomes in the GnomAD database, including 19,853 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 5601 hom., cov: 33)

Exomes 𝑓: 0.29 ( 14252 hom. )

Consequence

SCN4B
NM_174934.4 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.183

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 11-118134148-A-G is Benign according to our data. Variant chr11-118134148-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 302591.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
SCN4B	NM_174934.4 linkuse as main transcript	c.*2879T>C	3_prime_UTR_variant	5/5	ENST00000324727.9
SCN4B	NM_001142348.2 linkuse as main transcript	c.*2879T>C	3_prime_UTR_variant	3/3
SCN4B	NM_001142349.2 linkuse as main transcript	c.*2879T>C	3_prime_UTR_variant	4/4
SCN4B	NR_024527.2 linkuse as main transcript	n.3555T>C	non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCN4B	ENST00000324727.9 linkuse as main transcript	c.*2879T>C	3_prime_UTR_variant	5/5	1	NM_174934.4	P1	Q8IWT1-1
SCN4B	ENST00000415030.6 linkuse as main transcript	n.3709T>C	non_coding_transcript_exon_variant	4/4	1
SCN4B	ENST00000423160.2 linkuse as main transcript	n.3200T>C	non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes

AF:

0.243

AC:

36959

AN:

152106

Hom.:

5600

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0713

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.244

Gnomad ASJ

AF:

0.280

Gnomad EAS

AF:

0.0635

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.344

Gnomad OTH

AF:

0.244

GnomAD3 exomes

AF:

0.264

AC:

34496

AN:

130674

Hom.:

5207

AF XY:

0.264

AC XY:

18822

AN XY:

71220

show subpopulations

Gnomad AFR exome

AF:

0.0584

Gnomad AMR exome

AF:

0.261

Gnomad ASJ exome

AF:

0.273

Gnomad EAS exome

AF:

0.0513

Gnomad SAS exome

AF:

0.211

Gnomad FIN exome

AF:

0.355

Gnomad NFE exome

AF:

0.347

Gnomad OTH exome

AF:

0.271

GnomAD4 exome

AF:

0.293

AC:

88609

AN:

301926

Hom.:

14252

Cov.:

AF XY:

0.288

AC XY:

49534

AN XY:

172056

show subpopulations

Gnomad4 AFR exome

AF:

0.0690

Gnomad4 AMR exome

AF:

0.262

Gnomad4 ASJ exome

AF:

0.274

Gnomad4 EAS exome

AF:

0.0596

Gnomad4 SAS exome

AF:

0.218

Gnomad4 FIN exome

AF:

0.361

Gnomad4 NFE exome

AF:

0.351

Gnomad4 OTH exome

AF:

0.278

GnomAD4 genome

AF:

0.243

AC:

36967

AN:

152224

Hom.:

5601

Cov.:

AF XY:

0.240

AC XY:

17852

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.0712

Gnomad4 AMR

AF:

0.245

Gnomad4 ASJ

AF:

0.280

Gnomad4 EAS

AF:

0.0631

Gnomad4 SAS

AF:

0.211

Gnomad4 FIN

AF:

0.349

Gnomad4 NFE

AF:

0.344

Gnomad4 OTH

AF:

0.240

Alfa

AF:

0.277

Hom.:

1374

Bravo

AF:

0.227

Asia WGS

AF:

0.137

AC:

474

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

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

-0.89

CADD

Benign

1.2

DANN

Benign

0.49

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