chr12-51765796-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_014191.4(SCN8A):c.2670C>T(p.Ala890=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000632 in 1,613,962 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A890A) 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN8A | NM_001330260.2 | c.2670C>T | p.Ala890= | synonymous_variant | 16/27 | ENST00000627620.5 | |
SCN8A | NM_014191.4 | c.2670C>T | p.Ala890= | synonymous_variant | 16/27 | ENST00000354534.11 | |
SCN8A | NM_001177984.3 | c.2670C>T | p.Ala890= | synonymous_variant | 16/26 | ||
SCN8A | NM_001369788.1 | c.2670C>T | p.Ala890= | synonymous_variant | 16/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN8A | ENST00000354534.11 | c.2670C>T | p.Ala890= | synonymous_variant | 16/27 | 1 | NM_014191.4 | P4 | |
SCN8A | ENST00000627620.5 | c.2670C>T | p.Ala890= | synonymous_variant | 16/27 | 5 | NM_001330260.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000309 AC: 47AN: 152032Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000998 AC: 25AN: 250430Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135690
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461816Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727190
GnomAD4 genome ? AF: 0.000309 AC: 47AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74392
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 22, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 21, 2016 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 28, 2020 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at