chr11-123633965-C-A

Variant names:

• chr11-123633965-C-A
• rs1148111
• ENST00000530277.5:c.*178G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000530277.5(SCN3B):​c.*178G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SCN3B ENST00000530277.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 3 publications found

Genes affected

SCN3B (HGNC:20665): (sodium voltage-gated channel beta subunit 3) Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel beta subunit gene family, and influences the inactivation kinetics of the sodium channel. Two alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]

SCN3B Gene-Disease associations (from GenCC):

• familial atrial fibrillation

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Brugada syndrome 7

  Inheritance: AD, Unknown Classification: LIMITED Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
• Brugada syndrome 1

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000530277.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCN3B	NM_001040151.2	MANE Select	c.*22+156G>T		intron	N/A	NP_001035241.1	Q9NY72
	SCN3B	NM_018400.4		c.*22+156G>T		intron	N/A	NP_060870.1	Q9NY72

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCN3B	ENST00000530277.5	TSL:1	c.*178G>T		3_prime_UTR	Exon 6 of 6	ENSP00000432785.1	Q9NY72
	SCN3B	ENST00000299333.8	TSL:1 MANE Select	c.*22+156G>T		intron	N/A	ENSP00000299333.3	Q9NY72
	SCN3B	ENST00000392770.6	TSL:1	c.*22+156G>T		intron	N/A	ENSP00000376523.2	Q9NY72

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 489028 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 263784

African (AFR) AF: 0.00 AC: 0 AN: 14338

American (AMR) AF: 0.00 AC: 0 AN: 31530

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16236

East Asian (EAS) AF: 0.00 AC: 0 AN: 29072

South Asian (SAS) AF: 0.00 AC: 0 AN: 55570

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30290

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3588

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 281578

Other (OTH) AF: 0.00 AC: 0 AN: 26826

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.52
PhyloP100		-0.14

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

Other links and lift over

dbSNP: rs1148111; hg19: chr11-123504673;