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.5584G>T (p.Gly1862Cys)

CA1938381

240715 (ClinVar)

Gene: SCN3A
Condition: developmental and epileptic encephalopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 21ce5567-196f-4932-9651-2888968d7c02
Approved on: 2024-05-09
Published on: 2024-05-09

HGVS expressions

NM_006922.4:c.5584G>T
NM_006922.4(SCN3A):c.5584G>T (p.Gly1862Cys)
NC_000002.12:g.165090569C>A
CM000664.2:g.165090569C>A
NC_000002.11:g.165947079C>A
CM000664.1:g.165947079C>A
NC_000002.10:g.165655325C>A
NG_042289.1:g.118520G>T
ENST00000706067.1:c.5533G>T
ENST00000283254.12:c.5584G>T
ENST00000638473.1:c.*3425G>T
ENST00000639244.1:c.5521G>T
ENST00000640652.1:c.*2318G>T
ENST00000658209.1:c.3793G>T
ENST00000283254.11:c.5584G>T
ENST00000360093.7:c.5584G>T
ENST00000409101.7:c.5437G>T
NM_001081676.1:c.5437G>T
NM_001081677.1:c.5437G>T
NM_006922.3:c.5584G>T
NM_001081676.2:c.5437G>T
NM_001081677.2:c.5437G>T
More

Benign

Met criteria codes 2
PP3_Moderate BA1
Not Met criteria codes 14
BS4 BS3 BP4 BP1 BP7 PS1 PS2 PS3 PS4 PP1 PM5 PM6 PM2 PVS1

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.5584G>T variant in SCN3A is a missense variant predicted to case the substitution of glycine by cysteine at amino acid 1862 (p.Gly1862Cys). The highest population minor allele frequency in gnomAD v.2 is 8.2% (2915/35374 alleles) in the Latino population, which is higher than the ClinGen Epilepsy Sodium Channel threshold (0.3%) for BA1, and therefore meets this criterion (BA1). The computational predictor REVEL gives a score of 0.808 (PP3_Moderate). Although there are both pathogenic and benign types of evidence for this variant, the high frequency of this variant in gnomAD strongly supports a benign classification, and the only evidence in support of pathogenicity is based on a computational predictor that should not override the high population frequency, which precludes this variant from being pathogenic for a rare disease. In summary, this variant meets the criteria to be classified as Benign for autosomal dominant developmental and epileptic encephalopathy based on ACMG/AMP criteria applied, as specified by the ClinGen Epilepsy Sodium Channel VCEP: BA1 and PP3_Moderate. (VCEP specifications version 1; 6/27/2023).
Met criteria codes
PP3_Moderate
REVEL score of 0.8 above threshold
BA1
Highest MAF 8.2% MAF in gnomAD (2915/35374) including 130 homozygotes
Not Met criteria codes
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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