rs201243874
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001365536.1(SCN9A):c.205G>T(p.Gly69Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,612,448 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001365536.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN9A | NM_001365536.1 | c.205G>T | p.Gly69Cys | missense_variant | 2/27 | ENST00000642356.2 | NP_001352465.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN9A | ENST00000642356.2 | c.205G>T | p.Gly69Cys | missense_variant | 2/27 | NM_001365536.1 | ENSP00000495601.1 | |||
SCN9A | ENST00000303354.11 | c.205G>T | p.Gly69Cys | missense_variant | 2/27 | 5 | ENSP00000304748.7 | |||
SCN9A | ENST00000409672.5 | c.205G>T | p.Gly69Cys | missense_variant | 2/27 | 5 | ENSP00000386306.1 | |||
SCN9A | ENST00000645907.1 | c.205G>T | p.Gly69Cys | missense_variant | 2/27 | ENSP00000495983.1 | ||||
SCN9A | ENST00000454569.6 | c.205G>T | p.Gly69Cys | missense_variant | 2/15 | 1 | ENSP00000413212.2 | |||
SCN9A | ENST00000452182.2 | c.205G>T | p.Gly69Cys | missense_variant | 3/11 | 1 | ENSP00000393141.2 |
Frequencies
GnomAD3 genomes AF: 0.00000661 AC: 1AN: 151356Hom.: 0 Cov.: 24
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461092Hom.: 0 Cov.: 29 AF XY: 0.00000413 AC XY: 3AN XY: 726900
GnomAD4 genome AF: 0.00000661 AC: 1AN: 151356Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 73850
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at