rs758891499
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4BS1_SupportingBS2
The ENST00000354534.11(SCN8A):c.8C>T(p.Ala3Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,542 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. A3A) has been classified as Likely benign.
Frequency
Consequence
ENST00000354534.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN8A | NM_001330260.2 | c.8C>T | p.Ala3Val | missense_variant | 2/27 | ENST00000627620.5 | NP_001317189.1 | |
SCN8A | NM_014191.4 | c.8C>T | p.Ala3Val | missense_variant | 2/27 | ENST00000354534.11 | NP_055006.1 | |
SCN8A | NM_001177984.3 | c.8C>T | p.Ala3Val | missense_variant | 2/26 | NP_001171455.1 | ||
SCN8A | NM_001369788.1 | c.8C>T | p.Ala3Val | missense_variant | 2/26 | NP_001356717.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN8A | ENST00000354534.11 | c.8C>T | p.Ala3Val | missense_variant | 2/27 | 1 | NM_014191.4 | ENSP00000346534 | P4 | |
SCN8A | ENST00000627620.5 | c.8C>T | p.Ala3Val | missense_variant | 2/27 | 5 | NM_001330260.2 | ENSP00000487583 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000203 AC: 5AN: 246654Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134092
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461366Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726944
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74342
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2017 | The p.A3V variant (also known as c.8C>T), located in coding exon 1 of the SCN8A gene, results from a C to T substitution at nucleotide position 8. The alanine at codon 3 is replaced by valine, an amino acid with similar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Early infantile epileptic encephalopathy with suppression bursts Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 24, 2023 | This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 3 of the SCN8A protein (p.Ala3Val). This variant is present in population databases (rs758891499, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with SCN8A-related conditions. ClinVar contains an entry for this variant (Variation ID: 461351). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SCN8A protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at