rs200709238
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004588.5(SCN2B):c.498C>T(p.Val166Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,613,580 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00035 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000088 ( 0 hom. )
Consequence
SCN2B
NM_004588.5 synonymous
NM_004588.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.110
Genes affected
SCN2B (HGNC:10589): (sodium voltage-gated channel beta subunit 2) The protein encoded by this gene is the beta 2 subunit of the type II voltage-gated sodium channel. The encoded protein is involved in cell-cell adhesion and cell migration. Defects in this gene can be a cause of Brugada Syndrome, atrial fibrillation, or sudden infant death syndrome. [provided by RefSeq, Jul 2015]
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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=-0.51).
BP6
Variant 11-118167037-G-A is Benign according to our data. Variant chr11-118167037-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 515329.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.11 with no splicing effect.
BS2
High AC in GnomAd4 at 54 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN2B | NM_004588.5 | c.498C>T | p.Val166Val | synonymous_variant | 4/4 | ENST00000278947.6 | NP_004579.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN2B | ENST00000278947.6 | c.498C>T | p.Val166Val | synonymous_variant | 4/4 | 1 | NM_004588.5 | ENSP00000278947.5 | ||
SCN2B | ENST00000658882.1 | n.*323C>T | non_coding_transcript_exon_variant | 5/5 | ENSP00000499572.1 | |||||
SCN2B | ENST00000669850.1 | n.740C>T | non_coding_transcript_exon_variant | 4/4 | ||||||
SCN2B | ENST00000658882.1 | n.*323C>T | 3_prime_UTR_variant | 5/5 | ENSP00000499572.1 |
Frequencies
GnomAD3 genomes AF: 0.000355 AC: 54AN: 152134Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000203 AC: 51AN: 250882Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135666
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GnomAD4 exome AF: 0.0000876 AC: 128AN: 1461328Hom.: 0 Cov.: 31 AF XY: 0.0000839 AC XY: 61AN XY: 727034
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GnomAD4 genome AF: 0.000355 AC: 54AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74436
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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
Atrial fibrillation, familial, 14 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 28, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 07, 2021 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 29, 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
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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