2-165295929-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM1PP2BP4_Moderate
The NM_001040142.2(SCN2A):c.106A>G(p.Arg36Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000684 in 1,461,850 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. R36R) has been classified as Likely benign.
Frequency
Consequence
NM_001040142.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN2A | NM_001040142.2 | c.106A>G | p.Arg36Gly | missense_variant | 2/27 | ENST00000375437.7 | |
SCN2A | NM_001371246.1 | c.106A>G | p.Arg36Gly | missense_variant | 2/27 | ENST00000631182.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN2A | ENST00000375437.7 | c.106A>G | p.Arg36Gly | missense_variant | 2/27 | 5 | NM_001040142.2 | P1 | |
SCN2A | ENST00000631182.3 | c.106A>G | p.Arg36Gly | missense_variant | 2/27 | 5 | NM_001371246.1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251154Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135734
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461850Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727220
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Seizures, benign familial infantile, 3;C3150987:Developmental and epileptic encephalopathy, 11 Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 16, 2022 | 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 SCN2A 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. ClinVar contains an entry for this variant (Variation ID: 207035). This missense change has been observed in individuals with SCN2A-related conditions (PMID: 28379373, 30619928). This variant is present in population databases (rs796053167, gnomAD 0.0009%). This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 36 of the SCN2A protein (p.Arg36Gly). - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2023 | Reported as a maternally inherited variant in two unrelated patients with benign familial neonatal seizures (Wolff et al., 2017); Reported previously in a patient with neonatal seizures, however information about parental testing was not provided (Kong et al., 2019); Not observed at significant frequency in large population cohorts (gnomAD); This substitution is predicted to be within the N-terminal cytoplasmic domain; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Missense variants in this gene are often considered pathogenic (HGMD); This variant is associated with the following publications: (PMID: 35637276, 33731876, 30619928, 28379373) - |
Complex neurodevelopmental disorder Uncertain:1
Uncertain significance, no assertion criteria provided | provider interpretation | GenomeConnect - Simons Searchlight | Mar 18, 2019 | Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2019-03-18 and interpreted as Variant of Uncertain significance. Variant was initially reported on 2014-04-03 by GTR ID of laboratory name 26957. The reporting laboratory might also submit to ClinVar. Variant was identified in multiple siblings. Additional phenotypic information for other sibling(s) might be available from Simons Searchlight. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at