NM_001330260.2:c.3163C>T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP6BS2
The NM_001330260.2(SCN8A):c.3163C>T(p.Arg1055Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,120 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1055Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001330260.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN8A | NM_001330260.2 | c.3163C>T | p.Arg1055Trp | missense_variant | Exon 17 of 27 | ENST00000627620.5 | NP_001317189.1 | |
SCN8A | NM_014191.4 | c.3163C>T | p.Arg1055Trp | missense_variant | Exon 17 of 27 | ENST00000354534.11 | NP_055006.1 | |
SCN8A | NM_001177984.3 | c.3163C>T | p.Arg1055Trp | missense_variant | Exon 17 of 26 | NP_001171455.1 | ||
SCN8A | NM_001369788.1 | c.3163C>T | p.Arg1055Trp | missense_variant | Exon 17 of 26 | NP_001356717.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN8A | ENST00000354534.11 | c.3163C>T | p.Arg1055Trp | missense_variant | Exon 17 of 27 | 1 | NM_014191.4 | ENSP00000346534.4 | ||
SCN8A | ENST00000627620.5 | c.3163C>T | p.Arg1055Trp | missense_variant | Exon 17 of 27 | 5 | NM_001330260.2 | ENSP00000487583.2 | ||
SCN8A | ENST00000599343.5 | c.3196C>T | p.Arg1066Trp | missense_variant | Exon 16 of 26 | 5 | ENSP00000476447.3 | |||
SCN8A | ENST00000355133.7 | c.3163C>T | p.Arg1055Trp | missense_variant | Exon 16 of 25 | 1 | ENSP00000347255.4 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000445 AC: 11AN: 247140Hom.: 0 AF XY: 0.0000522 AC XY: 7AN XY: 134040
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1460918Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 726660
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
See cases Uncertain:1
ACMG classification criteria: PP2, PP3 -
Early infantile epileptic encephalopathy with suppression bursts Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at