chr2-166048865-A-G
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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
NM_001165963.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.295
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]
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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 |
---|---|---|---|---|---|---|---|
SCN1A | NM_001165963.4 | c.1028+21T>C | intron_variant | ENST00000674923.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN1A | ENST00000674923.1 | c.1028+21T>C | intron_variant | NM_001165963.4 | P4 | ||||
SCN1A-AS1 | ENST00000651574.1 | n.487+12735A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.487 AC: 73828AN: 151622Hom.: 18617 Cov.: 31
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GnomAD3 exomes AF: 0.524 AC: 130644AN: 249178Hom.: 34610 AF XY: 0.528 AC XY: 71095AN XY: 134714
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GnomAD4 exome AF: 0.528 AC: 704300AN: 1332654Hom.: 188176 Cov.: 21 AF XY: 0.530 AC XY: 355155AN XY: 670414
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GnomAD4 genome AF: 0.487 AC: 73852AN: 151742Hom.: 18620 Cov.: 31 AF XY: 0.488 AC XY: 36195AN XY: 74122
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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 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. - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | May 05, 2016 | Variant 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 submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jul 15, 2024 | This 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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at