rs199473137
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM2PM5PP2BP4
The NM_001099404.2(SCN5A):c.1918C>T(p.Pro640Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,156 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P640A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001099404.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN5A | NM_001099404.2 | c.1918C>T | p.Pro640Ser | missense_variant | 13/28 | ENST00000413689.6 | |
SCN5A | NM_000335.5 | c.1918C>T | p.Pro640Ser | missense_variant | 13/28 | ENST00000423572.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN5A | ENST00000413689.6 | c.1918C>T | p.Pro640Ser | missense_variant | 13/28 | 5 | NM_001099404.2 | P4 | |
SCN5A | ENST00000423572.7 | c.1918C>T | p.Pro640Ser | missense_variant | 13/28 | 1 | NM_000335.5 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 246780Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134096
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457156Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 723882
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at