rs1946892
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_006922.4(SCN3A):c.2031A>T(p.Thr677=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 1,613,204 control chromosomes in the GnomAD database, including 173,086 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T677T) has been classified as Likely benign.
Frequency
Consequence
NM_006922.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN3A | NM_006922.4 | c.2031A>T | p.Thr677= | synonymous_variant | 14/28 | ENST00000283254.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN3A | ENST00000283254.12 | c.2031A>T | p.Thr677= | synonymous_variant | 14/28 | 1 | NM_006922.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.519 AC: 78818AN: 151780Hom.: 21544 Cov.: 31
GnomAD3 exomes AF: 0.511 AC: 128191AN: 250954Hom.: 34778 AF XY: 0.502 AC XY: 68116AN XY: 135630
GnomAD4 exome AF: 0.448 AC: 653980AN: 1461306Hom.: 151513 Cov.: 46 AF XY: 0.450 AC XY: 326814AN XY: 726970
GnomAD4 genome ? AF: 0.519 AC: 78887AN: 151898Hom.: 21573 Cov.: 31 AF XY: 0.523 AC XY: 38796AN XY: 74230
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 20, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 13, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Epilepsy, familial focal, with variable foci 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Developmental and epileptic encephalopathy, 62 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at