2-166053185-A-G

Variant names:

• chr2-166053185-A-G
• rs2217199
• NM_001165963.4:c.603-242T>C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001165963.4(SCN1A):​c.603-242T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 760,782 control chromosomes in the GnomAD database, including 106,998 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.48 (18477 hom., cov: 33)
  • Exomes 𝑓: 0.54 (88521 hom.)
• Consequence: SCN1A NM_001165963.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.116

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 2-166053185-A-G is Benign according to our data. Variant chr2-166053185-A-G is described in ClinVar as [Benign]. Clinvar id is 669297.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCN1A	NM_001165963.4	c.603-242T>C		intron_variant	Intron 7 of 28	ENST00000674923.1	NP_001159435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCN1A	ENST00000674923.1	c.603-242T>C		intron_variant	Intron 7 of 28		NM_001165963.4	ENSP00000501589.1
SCN1A	ENST00000303395.9	c.603-242T>C		intron_variant	Intron 6 of 27	5		ENSP00000303540.4
SCN1A	ENST00000375405.7	c.603-242T>C		intron_variant	Intron 4 of 25	5		ENSP00000364554.3
SCN1A	ENST00000409050.1	c.603-242T>C		intron_variant	Intron 4 of 25	5		ENSP00000386312.1

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73565 AN: 151806 Hom.: 18477 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.481

GnomAD4 exome AF: 0.536 AC: 326405 AN: 608858 Hom.: 88521 AF XY: 0.536 AC XY: 175224 AN XY: 326682

Gnomad4 AFR exome AF: 0.347

Gnomad4 AMR exome AF: 0.455

Gnomad4 ASJ exome AF: 0.546

Gnomad4 EAS exome AF: 0.550

Gnomad4 SAS exome AF: 0.551

Gnomad4 FIN exome AF: 0.535

Gnomad4 NFE exome AF: 0.549

Gnomad4 OTH exome AF: 0.519

GnomAD4 genome AF: 0.484 AC: 73585 AN: 151924 Hom.: 18477 Cov.: 33 AF XY: 0.486 AC XY: 36075 AN XY: 74266

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.483

Alfa AF: 0.509 Hom.: 2505

Bravo AF: 0.469

Asia WGS AF: 0.542 AC: 1887 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Jul 31, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 42% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 39. Only high quality variants are reported. -

not provided Benign:1

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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	-0.83
CADD	Benign	0.67
DANN	Benign	0.45

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: rs2217199; hg19: chr2-166909695;