rs140990288
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BA1BP4
This summary comes from the ClinGen Evidence Repository: The c.3250G>A variant in SCN3A is a missense variant predicted to cause the subsitution of valine by isoleucine at amino acid 1084 (p.Val1084Ile). The variant is present in 0.5% of the total population, and 0.7% of the European (non-Finnish) population, in gnomAD v2.1.1, which exceeds the threshold of 0.01% for BA1. The in silico predictor REVEL score for this variant is 0.155 which meets the criteria for BP4_Moderate. The variant has not been reported in an individual with developmental and epileptic encepathalopathy in the reported literature to date, and does not fall within a pathogenic enriched region. In summary, this variant meets the criteria to be classified as benign for autosomal dominant developmental and epileptic encephalopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Epilepsy Sodium Channel VCEP: BA1, BP4_Moderate (specification v1.0; approved 6/27/23). LINK:https://erepo.genome.network/evrepo/ui/classification/CA214587/MONDO:0100062/069
Frequency
Consequence
NM_006922.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN3A | NM_006922.4 | c.3250G>A | p.Val1084Ile | missense_variant | 18/28 | ENST00000283254.12 | NP_008853.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN3A | ENST00000283254.12 | c.3250G>A | p.Val1084Ile | missense_variant | 18/28 | 1 | NM_006922.4 | ENSP00000283254 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00515 AC: 783AN: 152152Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00514 AC: 1293AN: 251398Hom.: 9 AF XY: 0.00526 AC XY: 715AN XY: 135870
GnomAD4 exome AF: 0.00783 AC: 11441AN: 1461840Hom.: 68 Cov.: 32 AF XY: 0.00766 AC XY: 5574AN XY: 727226
GnomAD4 genome AF: 0.00514 AC: 783AN: 152270Hom.: 3 Cov.: 32 AF XY: 0.00488 AC XY: 363AN XY: 74444
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2024 | SCN3A: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 04, 2019 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Nov 06, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 16, 2014 | - - |
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, reviewed by expert panel | curation | ClinGen Epilepsy Sodium Channel Variant Curation Expert Panel, Clingen | May 09, 2024 | The c.3250G>A variant in SCN3A is a missense variant predicted to cause the subsitution of valine by isoleucine at amino acid 1084 (p.Val1084Ile). The variant is present in 0.5% of the total population, and 0.7% of the European (non-Finnish) population, in gnomAD v2.1.1, which exceeds the threshold of 0.01% for BA1. The in silico predictor REVEL score for this variant is 0.155 which meets the criteria for BP4_Moderate. The variant has not been reported in an individual with developmental and epileptic encepathalopathy in the reported literature to date, and does not fall within a pathogenic enriched region. In summary, this variant meets the criteria to be classified as benign for autosomal dominant developmental and epileptic encephalopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Epilepsy Sodium Channel VCEP: BA1, BP4_Moderate (specification v1.0; approved 6/27/23). - |
Epilepsy, familial focal, with variable foci 4;C4693699:Developmental and epileptic encephalopathy, 62 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 22, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at