2-166242648-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001365536.1(SCN9A):c.3481T>C(p.Trp1161Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 1,548,672 control chromosomes in the GnomAD database, including 587,761 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001365536.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN9A | NM_001365536.1 | c.3481T>C | p.Trp1161Arg | missense_variant | Exon 19 of 27 | ENST00000642356.2 | NP_001352465.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN9A | ENST00000642356.2 | c.3481T>C | p.Trp1161Arg | missense_variant | Exon 19 of 27 | NM_001365536.1 | ENSP00000495601.1 | |||
SCN9A | ENST00000303354.11 | c.3481T>C | p.Trp1161Arg | missense_variant | Exon 19 of 27 | 5 | ENSP00000304748.7 | |||
SCN9A | ENST00000409672.5 | c.3448T>C | p.Trp1150Arg | missense_variant | Exon 19 of 27 | 5 | ENSP00000386306.1 | |||
SCN9A | ENST00000645907.1 | c.3448T>C | p.Trp1150Arg | missense_variant | Exon 19 of 27 | ENSP00000495983.1 |
Frequencies
GnomAD3 genomes AF: 0.878 AC: 133444AN: 151908Hom.: 58658 Cov.: 30
GnomAD3 exomes AF: 0.880 AC: 138994AN: 158010Hom.: 61211 AF XY: 0.878 AC XY: 72950AN XY: 83122
GnomAD4 exome AF: 0.870 AC: 1215240AN: 1396646Hom.: 529065 Cov.: 34 AF XY: 0.869 AC XY: 598906AN XY: 688988
GnomAD4 genome AF: 0.878 AC: 133538AN: 152026Hom.: 58696 Cov.: 30 AF XY: 0.877 AC XY: 65188AN XY: 74304
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jul 15, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 96% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 89. Only high quality variants are reported. - |
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 26, 2024 | - - |
Primary erythromelalgia Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Channelopathy-associated congenital insensitivity to pain, autosomal recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Generalized epilepsy with febrile seizures plus, type 7;C2752089:Neuropathy, hereditary sensory and autonomic, type 2A Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 04, 2025 | - - |
Paroxysmal extreme pain disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at