GeneBe

rs557140301

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BS2

The NM_001037.5(SCN1B):​c.-383_-366delGCCGCCGCCGCCGCCGCC variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000334 in 149,746 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000033 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SCN1B
NM_001037.5 upstream_gene

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18
Variant links:
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 made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BS2
High AC in GnomAd4 at 5 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCN1BNM_001037.5 linkc.-383_-366delGCCGCCGCCGCCGCCGCC upstream_gene_variant ENST00000262631.11 NP_001028.1 Q07699-1
SCN1BNM_199037.5 linkc.-383_-366delGCCGCCGCCGCCGCCGCC upstream_gene_variant NP_950238.1 Q07699-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCN1BENST00000262631.11 linkc.-383_-366delGCCGCCGCCGCCGCCGCC upstream_gene_variant 1 NM_001037.5 ENSP00000262631.3 Q07699-1
SCN1BENST00000415950.5 linkc.-383_-366delGCCGCCGCCGCCGCCGCC upstream_gene_variant 1 ENSP00000396915.2 Q07699-2
SCN1BENST00000638536.1 linkc.-383_-366delGCCGCCGCCGCCGCCGCC upstream_gene_variant 1 ENSP00000492022.1 Q07699-1

Frequencies

GnomAD3 genomes
AF:
0.0000334
AC:
5
AN:
149746
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000197
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0000984
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000447
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
32562
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
23448
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000334
AC:
5
AN:
149746
Hom.:
0
Cov.:
30
AF XY:
0.0000411
AC XY:
3
AN XY:
73014
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000197
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0000984
Gnomad4 NFE
AF:
0.0000447
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs557140301; hg19: chr19-35521341; API