Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!

Variant: NM_006922.4(SCN3A):c.3250G>A (p.Val1084Ile)

CA214587

194857 (ClinVar)

Gene: SCN3A
Condition: developmental and epileptic encephalopathy
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 187da753-159e-469c-ad28-c45f784fb8e0
Approved on: 2024-05-09
Published on: 2024-05-09

HGVS expressions

NM_006922.4:c.3250G>A
NM_006922.4(SCN3A):c.3250G>A (p.Val1084Ile)
NC_000002.12:g.165127774C>T
CM000664.2:g.165127774C>T
NC_000002.11:g.165984284C>T
CM000664.1:g.165984284C>T
NC_000002.10:g.165692530C>T
NG_042289.1:g.81315G>A
ENST00000706067.1:c.3199G>A
ENST00000283254.12:c.3250G>A
ENST00000638473.1:c.*1091G>A
ENST00000639244.1:c.3199G>A
ENST00000640652.1:c.3199G>A
ENST00000658209.1:c.1348G>A
ENST00000668657.1:c.3112G>A
ENST00000283254.11:c.3250G>A
ENST00000360093.7:c.3250G>A
ENST00000409101.7:c.3103G>A
ENST00000440431.6:c.3103G>A
ENST00000484898.1:n.19G>A
NM_001081676.1:c.3103G>A
NM_001081677.1:c.3103G>A
NM_006922.3:c.3250G>A
NM_001081676.2:c.3103G>A
NM_001081677.2:c.3103G>A
More

Benign

Met criteria codes 2
BA1 BP4
Not Met criteria codes 2
PS2 PM6

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Epilepsy Sodium Channel Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SCN3A Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Epilepsy Sodium Channel VCEP
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).
Met criteria codes
BA1
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.
BP4
The in-silico REVEL score for this variant is 0.155 which meets the criteria for BP4_Moderate.
Not Met criteria codes
PS2
This variant has not been identified as de novo in an individual with DEE in the reported literature to date.
PM6
This variant has not been identified as de novo in an individual with DEE in the reported literature to date.
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.