rs140990288

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BA1BP4

This summary comes from the ClinGen Evidence Repository: The c.3250G>A variant in SCN3A is a missense variant predicted to cause the subsitution of valine by isoleucine at amino acid 1084 (p.Val1084Ile). The variant is present in 0.5% of the total population, and 0.7% of the European (non-Finnish) population, in gnomAD v2.1.1, which exceeds the threshold of 0.01% for BA1. The in silico predictor REVEL score for this variant is 0.155 which meets the criteria for BP4_Moderate. The variant has not been reported in an individual with developmental and epileptic encepathalopathy in the reported literature to date, and does not fall within a pathogenic enriched region. In summary, this variant meets the criteria to be classified as benign for autosomal dominant developmental and epileptic encephalopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Epilepsy Sodium Channel VCEP: BA1, BP4_Moderate (specification v1.0; approved 6/27/23). LINK:https://erepo.genome.network/evrepo/ui/classification/CA214587/MONDO:0100062/069

Frequency

Genomes: 𝑓 0.0051 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0078 ( 68 hom. )

Consequence

SCN3A
NM_006922.4 missense

Scores

19

Clinical Significance

Benign reviewed by expert panel B:8

Conservation

PhyloP100: 0.0730
Variant links:
Genes affected
SCN3A (HGNC:10590): (sodium voltage-gated channel alpha subunit 3) Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family, and is found in a cluster of five alpha subunit genes on chromosome 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
For more information check the summary or visit ClinGen Evidence Repository.
BA1
For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SCN3ANM_006922.4 linkuse as main transcriptc.3250G>A p.Val1084Ile missense_variant 18/28 ENST00000283254.12 NP_008853.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SCN3AENST00000283254.12 linkuse as main transcriptc.3250G>A p.Val1084Ile missense_variant 18/281 NM_006922.4 ENSP00000283254 P1Q9NY46-3

Frequencies

GnomAD3 genomes
AF:
0.00515
AC:
783
AN:
152152
Hom.:
3
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00162
Gnomad AMI
AF:
0.0186
Gnomad AMR
AF:
0.00465
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00414
Gnomad FIN
AF:
0.00141
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00858
Gnomad OTH
AF:
0.00431
GnomAD3 exomes
AF:
0.00514
AC:
1293
AN:
251398
Hom.:
9
AF XY:
0.00526
AC XY:
715
AN XY:
135870
show subpopulations
Gnomad AFR exome
AF:
0.00105
Gnomad AMR exome
AF:
0.00544
Gnomad ASJ exome
AF:
0.0000992
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00542
Gnomad FIN exome
AF:
0.00217
Gnomad NFE exome
AF:
0.00731
Gnomad OTH exome
AF:
0.00702
GnomAD4 exome
AF:
0.00783
AC:
11441
AN:
1461840
Hom.:
68
Cov.:
32
AF XY:
0.00766
AC XY:
5574
AN XY:
727226
show subpopulations
Gnomad4 AFR exome
AF:
0.00116
Gnomad4 AMR exome
AF:
0.00548
Gnomad4 ASJ exome
AF:
0.000153
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00540
Gnomad4 FIN exome
AF:
0.00202
Gnomad4 NFE exome
AF:
0.00921
Gnomad4 OTH exome
AF:
0.00517
GnomAD4 genome
AF:
0.00514
AC:
783
AN:
152270
Hom.:
3
Cov.:
32
AF XY:
0.00488
AC XY:
363
AN XY:
74444
show subpopulations
Gnomad4 AFR
AF:
0.00161
Gnomad4 AMR
AF:
0.00464
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00414
Gnomad4 FIN
AF:
0.00141
Gnomad4 NFE
AF:
0.00859
Gnomad4 OTH
AF:
0.00427
Alfa
AF:
0.00704
Hom.:
7
Bravo
AF:
0.00522
TwinsUK
AF:
0.0121
AC:
45
ALSPAC
AF:
0.0112
AC:
43
ESP6500AA
AF:
0.00227
AC:
10
ESP6500EA
AF:
0.00791
AC:
68
ExAC
AF:
0.00550
AC:
668
Asia WGS
AF:
0.00260
AC:
9
AN:
3478
EpiCase
AF:
0.00720
EpiControl
AF:
0.00640

ClinVar

Significance: Benign
Submissions summary: Benign:8
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

not provided Benign:4
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenAug 01, 2024SCN3A: BP4, BS1, BS2 -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsFeb 04, 2019- -
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
not specified Benign:2
Likely benign, criteria provided, single submitterclinical testingGenomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of PhiladelphiaNov 06, 2015- -
Likely benign, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Jul 16, 2014- -
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, reviewed by expert panelcurationClinGen Epilepsy Sodium Channel Variant Curation Expert Panel, ClingenMay 09, 2024The c.3250G>A variant in SCN3A is a missense variant predicted to cause the subsitution of valine by isoleucine at amino acid 1084 (p.Val1084Ile). The variant is present in 0.5% of the total population, and 0.7% of the European (non-Finnish) population, in gnomAD v2.1.1, which exceeds the threshold of 0.01% for BA1. The in silico predictor REVEL score for this variant is 0.155 which meets the criteria for BP4_Moderate. The variant has not been reported in an individual with developmental and epileptic encepathalopathy in the reported literature to date, and does not fall within a pathogenic enriched region. In summary, this variant meets the criteria to be classified as benign for autosomal dominant developmental and epileptic encephalopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Epilepsy Sodium Channel VCEP: BA1, BP4_Moderate (specification v1.0; approved 6/27/23). -
Epilepsy, familial focal, with variable foci 4;C4693699:Developmental and epileptic encephalopathy, 62 Benign:1
Likely benign, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsApr 22, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.073
BayesDel_addAF
Benign
-0.54
T
BayesDel_noAF
Benign
-0.53
CADD
Benign
20
DANN
Benign
0.29
DEOGEN2
Benign
0.25
T;.;.;.;.
Eigen
Benign
-0.95
Eigen_PC
Benign
-0.69
FATHMM_MKL
Benign
0.19
N
LIST_S2
Benign
0.78
T;T;T;T;T
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.0054
T;T;T;T;T
MetaSVM
Benign
-0.97
T
MutationAssessor
Benign
-1.4
N;N;.;.;.
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Benign
0.42
T
PROVEAN
Benign
0.19
N;N;.;N;N
REVEL
Benign
0.15
Sift
Benign
0.96
T;T;.;T;T
Sift4G
Benign
0.83
T;T;.;T;T
Polyphen
0.0060
B;B;.;B;B
Vest4
0.050
MVP
0.26
MPC
0.55
ClinPred
0.0013
T
GERP RS
4.1
Varity_R
0.017
gMVP
0.33

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs140990288; hg19: chr2-165984284; COSMIC: COSV51826961; API