2-166198848-C-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001365536.1(SCN9A):āc.5791G>Cā(p.Asp1931His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000215 in 1,613,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001365536.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN9A | NM_001365536.1 | c.5791G>C | p.Asp1931His | missense_variant | 27/27 | ENST00000642356.2 | NP_001352465.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN9A | ENST00000642356.2 | c.5791G>C | p.Asp1931His | missense_variant | 27/27 | NM_001365536.1 | ENSP00000495601.1 | |||
SCN9A | ENST00000303354.11 | c.5791G>C | p.Asp1931His | missense_variant | 27/27 | 5 | ENSP00000304748.7 | |||
SCN9A | ENST00000409672.5 | c.5758G>C | p.Asp1920His | missense_variant | 27/27 | 5 | ENSP00000386306.1 | |||
SCN9A | ENST00000645907.1 | c.5758G>C | p.Asp1920His | missense_variant | 27/27 | ENSP00000495983.1 |
Frequencies
GnomAD3 genomes AF: 0.00126 AC: 191AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000273 AC: 68AN: 248784Hom.: 0 AF XY: 0.000244 AC XY: 33AN XY: 135004
GnomAD4 exome AF: 0.000107 AC: 156AN: 1461474Hom.: 0 Cov.: 32 AF XY: 0.000100 AC XY: 73AN XY: 727016
GnomAD4 genome AF: 0.00125 AC: 191AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.00124 AC XY: 92AN XY: 74424
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 26, 2017 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 27, 2017 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2020 | 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
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at