rs190664764
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_001365536.1(SCN9A):c.3361C>T(p.Arg1121Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00194 in 1,612,016 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1121Q) has been classified as Likely benign.
Frequency
Consequence
NM_001365536.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN9A | NM_001365536.1 | c.3361C>T | p.Arg1121Trp | missense_variant | 18/27 | ENST00000642356.2 | |
SCN1A-AS1 | NR_110260.1 | n.833G>A | non_coding_transcript_exon_variant | 7/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN9A | ENST00000642356.2 | c.3361C>T | p.Arg1121Trp | missense_variant | 18/27 | NM_001365536.1 | P1 | ||
SCN1A-AS1 | ENST00000651574.1 | n.1511G>A | non_coding_transcript_exon_variant | 14/19 |
Frequencies
GnomAD3 genomes ? AF: 0.00281 AC: 427AN: 151836Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00350 AC: 868AN: 247866Hom.: 11 AF XY: 0.00349 AC XY: 469AN XY: 134450
GnomAD4 exome AF: 0.00185 AC: 2707AN: 1460062Hom.: 28 Cov.: 31 AF XY: 0.00181 AC XY: 1315AN XY: 726276
GnomAD4 genome ? AF: 0.00281 AC: 427AN: 151954Hom.: 5 Cov.: 32 AF XY: 0.00440 AC XY: 327AN XY: 74272
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 02, 2014 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 03, 2016 | 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. - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 27, 2017 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Oct 07, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | SCN9A: BS1, BS2 - |
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 | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at