rs3812719

chr2-166053049-C-Achr2-166053049-C-Gchr2-166053049-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The NM_001165963.4(SCN1A):c.603-106G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 1,421,714 control chromosomes in the GnomAD database, including 353,248 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.67 (34169 hom., cov: 33)
  • Exomes 𝑓: 0.71 (319079 hom.)
• Consequence: SCN1A NM_001165963.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.31

Genes affected

SCN1A (HGNC:10585): (sodium voltage-gated channel alpha subunit 1) Voltage-dependent sodium channels are heteromeric complexes that regulate sodium exchange between intracellular and extracellular spaces and are essential for the generation and propagation of action potentials in muscle cells and neurons. Each sodium channel is composed of a large pore-forming, glycosylated alpha subunit and two smaller beta subunits. This gene encodes a sodium channel alpha subunit, which has four homologous domains, each of which contains six transmembrane regions. Allelic variants of this gene are associated with generalized epilepsy with febrile seizures and epileptic encephalopathy. Alternative splicing results in multiple transcript variants. The RefSeq Project has decided to create four representative RefSeq records. Three of the transcript variants are supported by experimental evidence and the fourth contains alternate 5' untranslated exons, the exact combination of which have not been experimentally confirmed for the full-length transcript. [provided by RefSeq, Oct 2015]

SCN1A-AS1 (HGNC:54069): (SCN1A and SCN9A antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BP6: Variant 2-166053049-C-A is Benign according to our data. Variant chr2-166053049-C-A is described in ClinVar as [Benign]. Clinvar id is 674938.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCN1A	NM_001165963.4	c.603-106G>T		intron_variant		ENST00000674923.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCN1A	ENST00000674923.1	c.603-106G>T		intron_variant			NM_001165963.4	P4
SCN1A-AS1	ENST00000651574.1	n.487+16919C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101163 AN: 151782 Hom.: 34141 Cov.: 33

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.637

GnomAD4 exome AF: 0.707 AC: 897554 AN: 1269814 Hom.: 319079 Cov.: 23 AF XY: 0.703 AC XY: 450921 AN XY: 641396

Gnomad4 AFR exome AF: 0.584

Gnomad4 AMR exome AF: 0.790

Gnomad4 ASJ exome AF: 0.605

Gnomad4 EAS exome AF: 0.896

Gnomad4 SAS exome AF: 0.686

Gnomad4 FIN exome AF: 0.749

Gnomad4 NFE exome AF: 0.703

Gnomad4 OTH exome AF: 0.687

GnomAD4 genome AF: 0.666 AC: 101235 AN: 151900 Hom.: 34169 Cov.: 33 AF XY: 0.672 AC XY: 49924 AN XY: 74256

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.640

Alfa AF: 0.670 Hom.: 9703

Bravo AF: 0.659

Asia WGS AF: 0.773 AC: 2688 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
Cadd	Benign	17
Dann	Benign	0.79

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: rs3812719; hg19: chr2-166909559;