19-35030823-G-T
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1PM2
The NM_001037.5(SCN1B):c.3G>T(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SCN1B
NM_001037.5 start_lost
NM_001037.5 start_lost
Scores
5
4
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.00
Publications
0 publications found
Genes affected
SCN1B (HGNC:10586): (sodium voltage-gated channel beta subunit 1) Voltage-gated sodium channels are heteromeric proteins that function in the generation and propagation of action potentials in muscle and neuronal cells. They are composed of one alpha and two beta subunits, where the alpha subunit provides channel activity and the beta-1 subunit modulates the kinetics of channel inactivation. This gene encodes a sodium channel beta-1 subunit. Mutations in this gene result in generalized epilepsy with febrile seizures plus, Brugada syndrome 5, and defects in cardiac conduction. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 10 ACMG points.
PVS1
Start lost variant, next in-frame start position is after 9 pathogenic variants. Next in-frame start position is after 34 codons. Genomic position: 35032587. Lost 0.152 part of the original CDS.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 936554Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0AN XY: 457422
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
936554
Hom.:
Cov.:
13
AF XY:
AC XY:
0
AN XY:
457422
African (AFR)
AF:
AC:
0
AN:
17416
American (AMR)
AF:
AC:
0
AN:
7138
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
10234
East Asian (EAS)
AF:
AC:
0
AN:
13558
South Asian (SAS)
AF:
AC:
0
AN:
40248
European-Finnish (FIN)
AF:
AC:
0
AN:
18206
Middle Eastern (MID)
AF:
AC:
0
AN:
2300
European-Non Finnish (NFE)
AF:
AC:
0
AN:
793180
Other (OTH)
AF:
AC:
0
AN:
34274
GnomAD4 genome
GnomAD4 genome
Cov.:
31
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
.;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Uncertain
D
PhyloP100
PROVEAN
Benign
N;.;N;.
REVEL
Uncertain
Sift
Benign
D;.;D;.
Sift4G
Pathogenic
D;.;D;D
Polyphen
B;B;B;B
Vest4
MutPred
Gain of sheet (P = 0.0477);Gain of sheet (P = 0.0477);Gain of sheet (P = 0.0477);Gain of sheet (P = 0.0477);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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