chr3-38587421-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_000335.5(SCN5A):c.2415G>A(p.Ser805Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000151 in 1,461,138 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000335.5 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN5A | NM_001099404.2 | c.2415G>A | p.Ser805Ser | synonymous_variant | Exon 15 of 28 | ENST00000413689.6 | NP_001092874.1 | |
SCN5A | NM_000335.5 | c.2415G>A | p.Ser805Ser | synonymous_variant | Exon 15 of 28 | ENST00000423572.7 | NP_000326.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN5A | ENST00000413689.6 | c.2415G>A | p.Ser805Ser | synonymous_variant | Exon 15 of 28 | 5 | NM_001099404.2 | ENSP00000410257.1 | ||
SCN5A | ENST00000423572.7 | c.2415G>A | p.Ser805Ser | synonymous_variant | Exon 15 of 28 | 1 | NM_000335.5 | ENSP00000398266.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248240Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134648
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461138Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 726792
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:2
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Cardiovascular phenotype Uncertain:1
The c.2415G>A variant (also known as p.S805S), located in coding exon 14 of the SCN5A gene, results from a G to A substitution at nucleotide position 2415. This nucleotide substitution does not change the serine at codon 805. This nucleotide position is poorly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration may result in the creation or strengthening of a novel splice donor site. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at