rs573936

Variant names:

• chr2-166083843-T-C
• rs573936
• NM_001165963.4:c.-141-6042A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001165963.4(SCN1A):​c.-141-6042A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,104 control chromosomes in the GnomAD database, including 6,409 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 0.29 (6409 hom., cov: 31)
• Consequence: SCN1A NM_001165963.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCN1A	NM_001165963.4	c.-141-6042A>G		intron_variant	Intron 2 of 28	ENST00000674923.1	NP_001159435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCN1A	ENST00000674923.1	c.-141-6042A>G		intron_variant	Intron 2 of 28		NM_001165963.4	ENSP00000501589.1
SCN1A	ENST00000303395.9	c.-141-6042A>G		intron_variant	Intron 1 of 27	5		ENSP00000303540.4
SCN1A	ENST00000409050.2	c.-187-5996A>G		intron_variant	Intron 1 of 27	5		ENSP00000386312.1

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43606 AN: 151986 Hom.: 6403 Cov.: 31

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.287 AC: 43654 AN: 152104 Hom.: 6409 Cov.: 31 AF XY: 0.290 AC XY: 21552 AN XY: 74344

African (AFR) AF: 0.331 AC: 13725 AN: 41484

American (AMR) AF: 0.284 AC: 4337 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1840 AN: 5170

South Asian (SAS) AF: 0.270 AC: 1301 AN: 4820

European-Finnish (FIN) AF: 0.307 AC: 3249 AN: 10594

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.260 AC: 17649 AN: 67992

Other (OTH) AF: 0.258 AC: 544 AN: 2108

Alfa AF: 0.270 Hom.: 667

Bravo AF: 0.290

Asia WGS AF: 0.292 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.51
PhyloP100		0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs573936; hg19: chr2-166940353; COSMIC: COSV71344289;