rs200870389
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_006514.4(SCN10A):c.2814C>T(p.Phe938=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000178 in 1,614,104 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00012 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00018 ( 1 hom. )
Consequence
SCN10A
NM_006514.4 synonymous
NM_006514.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.418
Genes affected
SCN10A (HGNC:10582): (sodium voltage-gated channel alpha subunit 10) The protein encoded by this gene is a tetrodotoxin-resistant voltage-gated sodium channel alpha subunit. The properties of the channel formed by the encoded transmembrane protein can be altered by interaction with different beta subunits. This protein may be involved in the onset of pain associated with peripheral neuropathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 3-38726879-G-A is Benign according to our data. Variant chr3-38726879-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 463244.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-38726879-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.418 with no splicing effect.
BS2
?
High AC in GnomAd4 at 19 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN10A | NM_006514.4 | c.2814C>T | p.Phe938= | synonymous_variant | 17/28 | ENST00000449082.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN10A | ENST00000449082.3 | c.2814C>T | p.Phe938= | synonymous_variant | 17/28 | 1 | NM_006514.4 | P4 | |
SCN10A | ENST00000655275.1 | c.2841C>T | p.Phe947= | synonymous_variant | 17/28 | ||||
SCN10A | ENST00000643924.1 | c.2814C>T | p.Phe938= | synonymous_variant | 16/27 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152220Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000239 AC: 60AN: 251350Hom.: 0 AF XY: 0.000272 AC XY: 37AN XY: 135834
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GnomAD4 exome AF: 0.000183 AC: 268AN: 1461884Hom.: 1 Cov.: 33 AF XY: 0.000220 AC XY: 160AN XY: 727244
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GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152220Hom.: 1 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74374
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Brugada syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 03, 2019 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2020 | This alteration is classified as 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. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at