rs781617696
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_014191.4(SCN8A):c.5760A>C(p.Thr1920=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,712 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T1920T) has been classified as Likely benign.
Frequency
Consequence
NM_014191.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN8A | NM_001330260.2 | c.5760A>C | p.Thr1920= | synonymous_variant | 27/27 | ENST00000627620.5 | |
SCN8A | NM_014191.4 | c.5760A>C | p.Thr1920= | synonymous_variant | 27/27 | ENST00000354534.11 | |
SCN8A | NM_001177984.3 | c.5637A>C | p.Thr1879= | synonymous_variant | 26/26 | ||
SCN8A | NM_001369788.1 | c.5637A>C | p.Thr1879= | synonymous_variant | 26/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN8A | ENST00000354534.11 | c.5760A>C | p.Thr1920= | synonymous_variant | 27/27 | 1 | NM_014191.4 | P4 | |
SCN8A | ENST00000627620.5 | c.5760A>C | p.Thr1920= | synonymous_variant | 27/27 | 5 | NM_001330260.2 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249238Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135208
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461712Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727138
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at