rs580041

chr2-166094000-C-T

Variant summary

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

The NM_001165963.4(SCN1A):c.-141-16199G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 151,840 control chromosomes in the GnomAD database, including 5,079 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 0.26 (5079 hom., cov: 32)
• Consequence: SCN1A NM_001165963.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCN1A	NM_001165963.4	c.-141-16199G>A		intron_variant		ENST00000674923.1
SCN1A-AS1	NR_110260.1	n.259+1337C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCN1A	ENST00000674923.1	c.-141-16199G>A		intron_variant			NM_001165963.4	P4
SCN1A-AS1	ENST00000651574.1	n.835+1337C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38934 AN: 151722 Hom.: 5076 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.257 AC: 38953 AN: 151840 Hom.: 5079 Cov.: 32 AF XY: 0.252 AC XY: 18676 AN XY: 74226

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.275

Alfa AF: 0.264 Hom.: 11072

Bravo AF: 0.255

Asia WGS AF: 0.216 AC: 750 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.59
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs580041; hg19: chr2-166950510;