rs602594

chr11-118169895-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004588.5(SCN2B):c.71-1144G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,104 control chromosomes in the GnomAD database, including 7,489 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (7489 hom., cov: 32)
• Consequence: SCN2B NM_004588.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCN2B	NM_004588.5	c.71-1144G>A		intron_variant		ENST00000278947.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCN2B	ENST00000278947.6	c.71-1144G>A		intron_variant		1	NM_004588.5	P1
SCN2B	ENST00000658882.1	c.174+424G>A		intron_variant, NMD_transcript_variant
SCN2B	ENST00000665446.1	n.306+424G>A		intron_variant, non_coding_transcript_variant
SCN2B	ENST00000669850.1	n.313-1144G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30690 AN: 151986 Hom.: 7481 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.0464

Gnomad FIN AF: 0.0304

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0375

Gnomad OTH AF: 0.152

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.202 AC: 30752 AN: 152104 Hom.: 7489 Cov.: 32 AF XY: 0.197 AC XY: 14628 AN XY: 74368

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0766

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.0304

Gnomad4 NFE AF: 0.0375

Gnomad4 OTH AF: 0.155

Alfa AF: 0.131 Hom.: 537

Bravo AF: 0.228

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.0
Dann	Benign	0.39

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

Other links and lift over

dbSNP: rs602594; hg19: chr11-118040610;