rs879253730

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7

The NM_001040151.2(SCN3B):c.423C>T(p.Ile141Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,892 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: not found (cov: 32)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

SCN3B
NM_001040151.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.01

Publications

0 publications found

Variant links:

Genes affected

SCN3B (HGNC:20665): (sodium voltage-gated channel beta subunit 3) Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit 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 beta subunit gene family, and influences the inactivation kinetics of the sodium channel. Two alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]

SCN3B Gene-Disease associations (from GenCC):

familial atrial fibrillation
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Brugada syndrome 7
Inheritance: AD, Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp
Brugada syndrome 1
Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

SCN3B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP6

Variant 11-123642468-G-A is Benign according to our data. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-123642468-G-A is described in CliVar as Likely_benign. Clinvar id is 1116932.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.01 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCN3B	NM_001040151.2 link	c.423C>T	p.Ile141Ile	synonymous_variant	Exon 4 of 7	ENST00000299333.8	NP_001035241.1	Q9NY72A0A024R3H7
SCN3B	NM_018400.4 link	c.423C>T	p.Ile141Ile	synonymous_variant	Exon 3 of 6		NP_060870.1	Q9NY72A0A024R3H7
SCN3B	XM_011542897.3 link	c.423C>T	p.Ile141Ile	synonymous_variant	Exon 4 of 7		XP_011541199.1	Q9NY72A0A024R3H7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCN3B	ENST00000299333.8 link	c.423C>T	p.Ile141Ile	synonymous_variant	Exon 4 of 7	1	NM_001040151.2	ENSP00000299333.3		Q9NY72

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000205

AC:

AN:

1461892

Hom.:

Cov.:

AF XY:

0.00000275

AC XY:

AN XY:

727246

show subpopulations

African (AFR)

AF:

0.0000299

AC:

AN:

33478

American (AMR)

AF:

0.00

AC:

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00

AC:

AN:

86258

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53420

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00000180

AC:

AN:

1112012

Other (OTH)

AF:

0.00

AC:

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

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.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Brugada syndrome 7

Benign:1

Jul 28, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

6.2

(source)

DANN

Benign

0.85

PhyloP100

2.0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over