Variant 11-118166849-G-A 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_004588.5(SCN2B):c.*38C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.092 in 1,611,098 control chromosomes in the GnomAD database, including 7,315 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.095 ( 738 hom., cov: 32)

Exomes 𝑓: 0.092 ( 6577 hom. )

Consequence

SCN2B
NM_004588.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.28

Variant links:

Genes affected

SCN2B (HGNC:10589): (sodium voltage-gated channel beta subunit 2) The protein encoded by this gene is the beta 2 subunit of the type II voltage-gated sodium channel. The encoded protein is involved in cell-cell adhesion and cell migration. Defects in this gene can be a cause of Brugada Syndrome, atrial fibrillation, or sudden infant death syndrome. [provided by RefSeq, Jul 2015]

SCN2B 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 (BayesDel_noAF=-0.81).

BP6

Variant 11-118166849-G-A is Benign according to our data. Variant chr11-118166849-G-A is described in ClinVar as [Benign]. Clinvar id is 1296386.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCN2B	NM_004588.5 linkuse as main transcript	c.*38C>T		3_prime_UTR_variant	4/4	ENST00000278947.6	NP_004579.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
SCN2B	ENST00000278947.6 linkuse as main transcript	c.*38C>T	3_prime_UTR_variant	4/4	1	NM_004588.5	ENSP00000278947	P1
SCN2B	ENST00000669850.1 linkuse as main transcript	n.928C>T	non_coding_transcript_exon_variant	4/4
SCN2B	ENST00000658882.1 linkuse as main transcript	c.*511C>T	3_prime_UTR_variant, NMD_transcript_variant	5/5			ENSP00000499572

Frequencies

GnomAD3 genomes

AF:

0.0955

AC:

14516

AN:

151958

Hom.:

738

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.0770

Gnomad ASJ

AF:

0.123

Gnomad EAS

AF:

0.0180

Gnomad SAS

AF:

0.0841

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.162

Gnomad NFE

AF:

0.0960

Gnomad OTH

AF:

0.103

GnomAD3 exomes

AF:

0.0875

AC:

21894

AN:

250108

Hom.:

1111

AF XY:

0.0898

AC XY:

12152

AN XY:

135300

show subpopulations

Gnomad AFR exome

AF:

0.104

Gnomad AMR exome

AF:

0.0479

Gnomad ASJ exome

AF:

0.111

Gnomad EAS exome

AF:

0.0211

Gnomad SAS exome

AF:

0.0832

Gnomad FIN exome

AF:

0.124

Gnomad NFE exome

AF:

0.100

Gnomad OTH exome

AF:

0.0990

GnomAD4 exome

AF:

0.0917

AC:

133749

AN:

1459022

Hom.:

6577

Cov.:

AF XY:

0.0918

AC XY:

66636

AN XY:

725970

show subpopulations

Gnomad4 AFR exome

AF:

0.101

Gnomad4 AMR exome

AF:

0.0508

Gnomad4 ASJ exome

AF:

0.114

Gnomad4 EAS exome

AF:

0.0126

Gnomad4 SAS exome

AF:

0.0835

Gnomad4 FIN exome

AF:

0.127

Gnomad4 NFE exome

AF:

0.0938

Gnomad4 OTH exome

AF:

0.0975

GnomAD4 genome

AF:

0.0955

AC:

14516

AN:

152076

Hom.:

738

Cov.:

AF XY:

0.0968

AC XY:

7198

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.0769

Gnomad4 ASJ

AF:

0.123

Gnomad4 EAS

AF:

0.0178

Gnomad4 SAS

AF:

0.0835

Gnomad4 FIN

AF:

0.127

Gnomad4 NFE

AF:

0.0960

Gnomad4 OTH

AF:

0.102

Alfa

AF:

0.0989

Hom.:

182

Bravo

AF:

0.0904

Asia WGS

AF:

0.0490

AC:

170

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 13, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.8

DANN

Benign

0.60

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