rs142217269
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The ENST00000449082.3(SCN10A):c.4568G>A(p.Cys1523Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00206 in 1,614,208 control chromosomes in the GnomAD database, including 6 homozygotes. 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. C1523R) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000449082.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN10A | NM_006514.4 | c.4568G>A | p.Cys1523Tyr | missense_variant | 27/28 | ENST00000449082.3 | NP_006505.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN10A | ENST00000449082.3 | c.4568G>A | p.Cys1523Tyr | missense_variant | 27/28 | 1 | NM_006514.4 | ENSP00000390600 | P4 | |
SCN10A | ENST00000655275.1 | c.4592G>A | p.Cys1531Tyr | missense_variant | 27/28 | ENSP00000499510 | ||||
SCN10A | ENST00000643924.1 | c.4565G>A | p.Cys1522Tyr | missense_variant | 26/27 | ENSP00000495595 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00128 AC: 195AN: 152242Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00115 AC: 288AN: 251228Hom.: 0 AF XY: 0.00109 AC XY: 148AN XY: 135770
GnomAD4 exome AF: 0.00215 AC: 3136AN: 1461848Hom.: 5 Cov.: 31 AF XY: 0.00199 AC XY: 1449AN XY: 727216
GnomAD4 genome AF: 0.00128 AC: 195AN: 152360Hom.: 1 Cov.: 33 AF XY: 0.00121 AC XY: 90AN XY: 74504
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | SCN10A: BS1 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 21, 2020 | This variant is associated with the following publications: (PMID: 25053638, 26733327, 25691538, 25691686, 23115331, 25250524, 28074886) - |
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jun 17, 2024 | - - |
SCN10A-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 05, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Brugada syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2019 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at