chr2-166048865-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001165963.4(SCN1A):​c.1028+21T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 1,484,396 control chromosomes in the GnomAD database, including 206,796 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.49 ( 18620 hom., cov: 31)
Exomes 𝑓: 0.53 ( 188176 hom. )

Consequence

SCN1A
NM_001165963.4 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.295
Variant links:
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)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 2-166048865-A-G is Benign according to our data. Variant chr2-166048865-A-G is described in ClinVar as [Benign]. Clinvar id is 496114.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SCN1ANM_001165963.4 linkuse as main transcriptc.1028+21T>C intron_variant ENST00000674923.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SCN1AENST00000674923.1 linkuse as main transcriptc.1028+21T>C intron_variant NM_001165963.4 P4P35498-1
SCN1A-AS1ENST00000651574.1 linkuse as main transcriptn.487+12735A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.487
AC:
73828
AN:
151622
Hom.:
18617
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.350
Gnomad AMI
AF:
0.583
Gnomad AMR
AF:
0.507
Gnomad ASJ
AF:
0.540
Gnomad EAS
AF:
0.557
Gnomad SAS
AF:
0.556
Gnomad FIN
AF:
0.536
Gnomad MID
AF:
0.446
Gnomad NFE
AF:
0.544
Gnomad OTH
AF:
0.483
GnomAD3 exomes
AF:
0.524
AC:
130644
AN:
249178
Hom.:
34610
AF XY:
0.528
AC XY:
71095
AN XY:
134714
show subpopulations
Gnomad AFR exome
AF:
0.348
Gnomad AMR exome
AF:
0.502
Gnomad ASJ exome
AF:
0.539
Gnomad EAS exome
AF:
0.576
Gnomad SAS exome
AF:
0.553
Gnomad FIN exome
AF:
0.535
Gnomad NFE exome
AF:
0.537
Gnomad OTH exome
AF:
0.514
GnomAD4 exome
AF:
0.528
AC:
704300
AN:
1332654
Hom.:
188176
Cov.:
21
AF XY:
0.530
AC XY:
355155
AN XY:
670414
show subpopulations
Gnomad4 AFR exome
AF:
0.332
Gnomad4 AMR exome
AF:
0.505
Gnomad4 ASJ exome
AF:
0.539
Gnomad4 EAS exome
AF:
0.554
Gnomad4 SAS exome
AF:
0.546
Gnomad4 FIN exome
AF:
0.537
Gnomad4 NFE exome
AF:
0.534
Gnomad4 OTH exome
AF:
0.519
GnomAD4 genome
AF:
0.487
AC:
73852
AN:
151742
Hom.:
18620
Cov.:
31
AF XY:
0.488
AC XY:
36195
AN XY:
74122
show subpopulations
Gnomad4 AFR
AF:
0.349
Gnomad4 AMR
AF:
0.508
Gnomad4 ASJ
AF:
0.540
Gnomad4 EAS
AF:
0.557
Gnomad4 SAS
AF:
0.556
Gnomad4 FIN
AF:
0.536
Gnomad4 NFE
AF:
0.544
Gnomad4 OTH
AF:
0.486
Alfa
AF:
0.522
Hom.:
25132
Bravo
AF:
0.475
Asia WGS
AF:
0.543
AC:
1887
AN:
3472

ClinVar

Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Benign, criteria provided, single submitterclinical testingGeneDxJun 14, 2018This 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. -
Benign, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpMay 05, 2016Variant summary: The SCN1A c.1028+21T>C variant affects a non-conserved intronic nucleotide. Mutation taster predicts a benign outcome for this variant. This variant was found in 62812/119682 control chromosomes (16581 homozygotes) at a frequency of 0.5248241, which greatly exceeds the maximal expected frequency of a pathogenic SCN1A allele (0.0000179), suggesting this variant is benign. Moreover, the variant was found in an internal sample to co-occur with a pathogenic truncating SCN1A variant, further supporting neutrality. Additionally, several independent peer reviewed publications classified the variant as a polymorphism. Taken together, this variant was classified as Benign. -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingUnidad de Genómica Garrahan, Hospital de Pediatría GarrahanJul 15, 2024This variant is classified as Benign based on local population frequency. This variant was detected in 73% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 68. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
6.3
DANN
Benign
0.50

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1542484; hg19: chr2-166905375; COSMIC: COSV57684001; API