Genetic Variant SCN1B:p.Gly10Val (chr19-35030849-G-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001037.5(SCN1B):c.29G>T(p.Gly10Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000123 in 813,306 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G10S) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 31)

Exomes 𝑓: 0.0000012 ( 0 hom. )

Consequence

SCN1B
NM_001037.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0420

Publications

0 publications found

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]

SCN1B links:

HPN-AS1 (HGNC:47041): (HPN antisense RNA 1)

HPN-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001037.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCN1B	NM_001037.5	MANE Select	c.29G>T	p.Gly10Val	missense	Exon 1 of 6	NP_001028.1
	SCN1B	NM_199037.5		c.29G>T	p.Gly10Val	missense	Exon 1 of 3	NP_950238.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
SCN1B	ENST00000262631.11	TSL:1 MANE Select	c.29G>T	p.Gly10Val	missense	Exon 1 of 6	ENSP00000262631.3
SCN1B	ENST00000415950.5	TSL:1	c.29G>T	p.Gly10Val	missense	Exon 1 of 3	ENSP00000396915.2
SCN1B	ENST00000638536.1	TSL:1	c.29G>T	p.Gly10Val	missense	Exon 1 of 5	ENSP00000492022.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000123

AC:

AN:

813306

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

389902

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

15544

American (AMR)

AF:

0.00

AC:

AN:

4358

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

7974

East Asian (EAS)

AF:

0.00

AC:

AN:

12134

South Asian (SAS)

AF:

0.00

AC:

AN:

21964

European-Finnish (FIN)

AF:

0.00

AC:

AN:

14218

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1938

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

705492

Other (OTH)

AF:

0.0000337

AC:

AN:

29684

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.073

BayesDel_addAF

Uncertain

0.13

BayesDel_noAF

Uncertain

-0.050

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.074

Eigen

Benign

0.13

Eigen_PC

Benign

0.072

FATHMM_MKL

Uncertain

0.77

LIST_S2

Benign

0.47

M_CAP

Pathogenic

0.98

MetaRNN

Uncertain

0.44

MetaSVM

Uncertain

0.56

MutationAssessor

Benign

0.0

PhyloP100

0.042

PrimateAI

Pathogenic

0.85

PROVEAN

Benign

-0.61

REVEL

Uncertain

0.40

Sift

Benign

0.46

Sift4G

Benign

0.51

Polyphen

0.99

Vest4

0.20

MutPred

0.35

Loss of sheet (P = 0.0228)

MVP

0.99

MPC

0.84

ClinPred

0.33

GERP RS

3.2

PromoterAI

0.049

Neutral

(source)

Varity_R

0.12

gMVP

0.51

Mutation Taster

=84/16

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over