rs67701503

Positions:

chr19-35034035-C-A

Variant summary

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

The ENST00000415950.5(SCN1B):c.744C>A(p.Ser248Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 1,549,658 control chromosomes in the GnomAD database, including 16,941 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S248I) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.14 ( 1552 hom., cov: 31)

Exomes 𝑓: 0.14 ( 15389 hom. )

Consequence

SCN1B
ENST00000415950.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.294

Variant links:

Genes affected

SCN1B (HGNC:10586): (sodium voltage-gated channel beta subunit 1) Voltage-gated sodium channels are heteromeric proteins that function in the generation and propagation of action potentials in muscle and neuronal cells. They are composed of one alpha and two beta subunits, where the alpha subunit provides channel activity and the beta-1 subunit modulates the kinetics of channel inactivation. This gene encodes a sodium channel beta-1 subunit. Mutations in this gene result in generalized epilepsy with febrile seizures plus, Brugada syndrome 5, and defects in cardiac conduction. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]

SCN1B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001129061).

BP6

Variant 19-35034035-C-A is Benign according to our data. Variant chr19-35034035-C-A is described in ClinVar as [Benign]. Clinvar id is 138999.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-35034035-C-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SCN1B	NM_001037.5 linkuse as main transcript	c.448+296C>A		intron_variant		ENST00000262631.11
SCN1B	NM_199037.5 linkuse as main transcript	c.744C>A	p.Ser248Arg	missense_variant	3/3
SCN1B	NM_001321605.2 linkuse as main transcript	c.349+296C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCN1B	ENST00000262631.11 linkuse as main transcript	c.448+296C>A		intron_variant		1	NM_001037.5	P1	Q07699-1

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

21339

AN:

151926

Hom.:

1555

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0910

Gnomad AMI

AF:

0.117

Gnomad AMR

AF:

0.135

Gnomad ASJ

AF:

0.259

Gnomad EAS

AF:

0.197

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.170

GnomAD3 exomes

AF:

0.146

AC:

22627

AN:

154816

Hom.:

1816

AF XY:

0.147

AC XY:

11994

AN XY:

81778

show subpopulations

Gnomad AFR exome

AF:

0.0891

Gnomad AMR exome

AF:

0.0884

Gnomad ASJ exome

AF:

0.256

Gnomad EAS exome

AF:

0.213

Gnomad SAS exome

AF:

0.114

Gnomad FIN exome

AF:

0.183

Gnomad NFE exome

AF:

0.152

Gnomad OTH exome

AF:

0.156

GnomAD4 exome

AF:

0.144

AC:

201504

AN:

1397614

Hom.:

15389

Cov.:

AF XY:

0.145

AC XY:

99781

AN XY:

689434

show subpopulations

Gnomad4 AFR exome

AF:

0.0899

Gnomad4 AMR exome

AF:

0.0939

Gnomad4 ASJ exome

AF:

0.263

Gnomad4 EAS exome

AF:

0.195

Gnomad4 SAS exome

AF:

0.119

Gnomad4 FIN exome

AF:

0.180

Gnomad4 NFE exome

AF:

0.142

Gnomad4 OTH exome

AF:

0.156

GnomAD4 genome

AF:

0.140

AC:

21333

AN:

152044

Hom.:

1552

Cov.:

AF XY:

0.142

AC XY:

10543

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.0910

Gnomad4 AMR

AF:

0.135

Gnomad4 ASJ

AF:

0.259

Gnomad4 EAS

AF:

0.197

Gnomad4 SAS

AF:

0.116

Gnomad4 FIN

AF:

0.189

Gnomad4 NFE

AF:

0.155

Gnomad4 OTH

AF:

0.169

Alfa

AF:

0.158

Hom.:

3204

Bravo

AF:

0.136

TwinsUK

AF:

0.132

AC:

488

ALSPAC

AF:

0.146

AC:

562

ESP6500AA

AF:

0.0844

AC:

190

ESP6500EA

AF:

0.146

AC:

640

ExAC

AF:

0.0943

AC:

3981

Asia WGS

AF:

0.116

AC:

401

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:6

Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	research	Biesecker Lab/Clinical Genomics Section, National Institutes of Health	Jun 24, 2013	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 22, 2013	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. -
Benign, criteria provided, single submitter	clinical testing	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	Jul 31, 2024	This variant is classified as Benign based on local population frequency. This variant was detected in 32% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 30. Only high quality variants are reported. -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -

Brugada syndrome 5

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_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.43

CADD

Benign

DANN

Uncertain

0.99

Eigen

Benign

-0.78

Eigen_PC

Benign

-0.83

FATHMM_MKL

Benign

0.22

LIST_S2

Benign

0.42

T;T

MetaRNN

Benign

0.0011

T;T

MetaSVM

Benign

-0.99

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.040

N;.

REVEL

Benign

0.11

Sift

Pathogenic

0.0

D;.

Polyphen

0.0020

B;.

Vest4

0.11

MutPred

0.26

Gain of sheet (P = 0.0149);.;

MPC

1.3

ClinPred

0.039

GERP RS

1.9

gMVP

0.24

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