rs2165179

chr2-165183208-G-Achr2-165183208-G-C

Variant summary

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

The NM_006922.4(SCN3A):c.-51+3343C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,150 control chromosomes in the GnomAD database, including 1,727 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 0.11 (1727 hom., cov: 32)
• Consequence: SCN3A NM_006922.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51

Genes affected

SCN3A (HGNC:10590): (sodium voltage-gated channel alpha subunit 3) Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains 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 alpha subunit gene family, and is found in a cluster of five alpha subunit genes on chromosome 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCN3A	NM_006922.4	c.-51+3343C>T		intron_variant		ENST00000283254.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCN3A	ENST00000283254.12	c.-51+3343C>T		intron_variant		1	NM_006922.4	P1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16620 AN: 152032 Hom.: 1710 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.0475

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0534

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0416

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.109 AC: 16656 AN: 152150 Hom.: 1727 Cov.: 32 AF XY: 0.115 AC XY: 8583 AN XY: 74382

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.0475

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0534

Gnomad4 NFE AF: 0.0416

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0687 Hom.: 147

Bravo AF: 0.132

Asia WGS AF: 0.307 AC: 1062 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	9.0
Dann	Benign	0.59

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: rs2165179; hg19: chr2-166039718;