3-38609810-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_000335.5(SCN5A):c.858G>A(p.Ala286Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000694 in 1,613,926 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A286A) has been classified as Likely benign.
Frequency
Consequence
NM_000335.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN5A | NM_001099404.2 | c.858G>A | p.Ala286Ala | synonymous_variant | Exon 7 of 28 | ENST00000413689.6 | NP_001092874.1 | |
SCN5A | NM_000335.5 | c.858G>A | p.Ala286Ala | synonymous_variant | Exon 7 of 28 | ENST00000423572.7 | NP_000326.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN5A | ENST00000413689.6 | c.858G>A | p.Ala286Ala | synonymous_variant | Exon 7 of 28 | 5 | NM_001099404.2 | ENSP00000410257.1 | ||
SCN5A | ENST00000423572.7 | c.858G>A | p.Ala286Ala | synonymous_variant | Exon 7 of 28 | 1 | NM_000335.5 | ENSP00000398266.2 |
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000762 AC: 19AN: 249256Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135226
GnomAD4 exome AF: 0.0000452 AC: 66AN: 1461558Hom.: 0 Cov.: 31 AF XY: 0.0000371 AC XY: 27AN XY: 727070
GnomAD4 genome AF: 0.000302 AC: 46AN: 152368Hom.: 0 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74512
ClinVar
Submissions by phenotype
not provided Benign:3
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Cardiac arrhythmia Benign:2
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not specified Benign:1
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Cardiovascular phenotype Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at