rs146878122
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 5P and 7B. PM1PM5PP2BP4_ModerateBP6BS2
The NM_001165963.4(SCN1A):c.3899C>T(p.Thr1300Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000996 in 1,606,822 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 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. T1300R) has been classified as Pathogenic.
Frequency
Consequence
NM_001165963.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN1A | NM_001165963.4 | c.3899C>T | p.Thr1300Ile | missense_variant | 23/29 | ENST00000674923.1 | |
LOC102724058 | NR_110598.1 | n.176-5791G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN1A | ENST00000674923.1 | c.3899C>T | p.Thr1300Ile | missense_variant | 23/29 | NM_001165963.4 | P4 | ||
SCN1A-AS1 | ENST00000651574.1 | n.193-5791G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000192 AC: 29AN: 150880Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000156 AC: 39AN: 250156Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135212
GnomAD4 exome AF: 0.0000900 AC: 131AN: 1455826Hom.: 1 Cov.: 30 AF XY: 0.000102 AC XY: 74AN XY: 724346
GnomAD4 genome AF: 0.000192 AC: 29AN: 150996Hom.: 0 Cov.: 32 AF XY: 0.000230 AC XY: 17AN XY: 73778
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 02, 2020 | This variant is associated with the following publications: (PMID: 29948376) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 16, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | SCN1A: PP2, BS2 - |
not specified Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jan 11, 2023 | Variant summary: SCN1A c.3899C>T (p.Thr1300Ile) results in a non-conservative amino acid change located in the ion transport domain (IPR005821) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00016 in 250156 control chromosomes (gnomAD). The observed variant frequency is approximately 9 fold of the estimated maximal expected allele frequency for a pathogenic variant in SCN1A causing SCN1A-Related Seizure Disorder phenotype (1.8e-05), strongly suggesting that the variant is benign. c.3899C>T has been reported in the literature in the heterozygous state in twin siblings affected with juvenile myoclonic epilepsy, however both parents also carried the variant and were unaffected (Landoulsi_2018). The siblings and mother from this family were also heterozygous for a variant in MAST4 (c.4486G>A, p.Val1496Met), but without strong evidence for pathogenicity. Thus this report does not provide unequivocal conclusions about association of c.3899C>T with SCN1A-Related Seizure Disorder. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Seven submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified it as either likely benign (n=4) or VUS (n=3). Based on the evidence outlined above, the variant was classified as likely benign. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 02, 2017 | - - |
Intellectual disability Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille | Jan 01, 2019 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 15, 2021 | This alteration is classified as likely 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
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2024 | - - |
Severe myoclonic epilepsy in infancy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at