rs762966087
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001365536.1(SCN9A):c.576T>C(p.Asp192Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,613,400 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 (★★).
Frequency
Consequence
NM_001365536.1 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN9A | NM_001365536.1 | c.576T>C | p.Asp192Asp | synonymous_variant | Exon 5 of 27 | ENST00000642356.2 | NP_001352465.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN9A | ENST00000642356.2 | c.576T>C | p.Asp192Asp | synonymous_variant | Exon 5 of 27 | NM_001365536.1 | ENSP00000495601.1 | |||
SCN9A | ENST00000303354.11 | c.576T>C | p.Asp192Asp | synonymous_variant | Exon 5 of 27 | 5 | ENSP00000304748.7 | |||
SCN9A | ENST00000409672.5 | c.576T>C | p.Asp192Asp | synonymous_variant | Exon 5 of 27 | 5 | ENSP00000386306.1 | |||
SCN9A | ENST00000645907.1 | c.576T>C | p.Asp192Asp | synonymous_variant | Exon 5 of 27 | ENSP00000495983.1 | ||||
SCN9A | ENST00000454569.6 | c.576T>C | p.Asp192Asp | synonymous_variant | Exon 5 of 15 | 1 | ENSP00000413212.2 | |||
SCN9A | ENST00000452182.2 | c.576T>C | p.Asp192Asp | synonymous_variant | Exon 6 of 11 | 1 | ENSP00000393141.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152068Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248934Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135070
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1461332Hom.: 0 Cov.: 33 AF XY: 0.0000330 AC XY: 24AN XY: 726946
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152068Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74278
ClinVar
Submissions by phenotype
Inborn genetic diseases 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. -
Generalized epilepsy with febrile seizures plus, type 7;C2752089:Neuropathy, hereditary sensory and autonomic, type 2A Benign:1
- -
not provided Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at