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_001040142.2(SCN2A):c.56G>A (p.Arg19Lys)

CA155062

130224 (ClinVar)

Gene: SCN2A
Condition: complex neurodevelopmental disorder
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: d0d6e462-b592-46d2-81f7-7a088d5b77be
Approved on: 2024-05-07
Published on: 2024-05-08

HGVS expressions

NM_001040142.2:c.56G>A
NM_001040142.2(SCN2A):c.56G>A (p.Arg19Lys)
NC_000002.12:g.165295879G>A
CM000664.2:g.165295879G>A
NC_000002.11:g.166152389G>A
CM000664.1:g.166152389G>A
NC_000002.10:g.165860635G>A
NG_008143.1:g.61478G>A
ENST00000631182.3:c.56G>A
ENST00000375437.7:c.56G>A
ENST00000635945.1:n.419G>A
ENST00000636071.2:c.56G>A
ENST00000636135.1:c.56G>A
ENST00000636384.2:c.56G>A
ENST00000636662.2:c.56G>A
ENST00000636769.1:c.56G>A
ENST00000636985.2:c.-552-1G>A
ENST00000637266.2:c.56G>A
ENST00000637367.1:c.56G>A
ENST00000638151.1:n.141-1G>A
ENST00000283256.10:c.56G>A
ENST00000375427.4:c.56G>A
ENST00000375437.6:c.56G>A
ENST00000424833.5:c.56G>A
ENST00000480032.4:n.199G>A
ENST00000631182.2:c.56G>A
NM_001040142.1:c.56G>A
NM_001040143.1:c.56G>A
NM_021007.2:c.56G>A
NM_001040143.2:c.56G>A
NM_001371246.1:c.56G>A
NM_001371247.1:c.56G>A
NM_021007.3:c.56G>A
More

Benign

Met criteria codes 1
BA1
Not Met criteria codes 10
PM5 PM1 PM6 BS3 BP4 PS3 PS2 PS1 PP4 PP3

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 SCN2A Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Epilepsy Sodium Channel VCEP
The c.56G>A variant in SCN2A is a missense variant predicted to cause substitution of arginine by lysine at amino acid 19 (p.Arg19Lys). This variant is present at an allele frequency of 8% of the total population in gnomAD (v2.1.1), with the highest sub-population allele frequency in the East Asian population with an AF of 15%, which exceeds the threshold of 0.01% to meet the stand-alone criterion for Benign (BA1). This variant has not been reported in the literature to date in an individual with a complex neurodevelopmental disorder (PS2_not met, PM6_not met, PS4_not met). The variant has not been functionally characterized, and is not located in a pathogenic enriched region defined as a mutational hotspot (PM1_not met). In summary, this variant meets the criteria to be classified as BENIGN for AUTOSOMAL DOMINANT COMPLEX NEURODEVELOPMENTAL DISORDER based on the ACMG/AMP criteria applied, as specified by the ClinGen Epilepsy Sodium Channel VCEP: BA1 (Epilepsy Sodium Channel VCEP specifications, version 1.0; approved 6/13/23).
Met criteria codes
BA1
This variant is present at an allele frequency of 8% of the total population in gnomAD (v2.1.1), which exceeds the threshold of 0.01% to meet BA1.
Not Met criteria codes
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
This variant is not located in a pathogenic enriched region.
PM6
To date, this variant has not been reported in the literature as de novo in an individual with a complex neurodevelopmental disorder.
BS3
This variant has not been functionally characterized to date. Furthermore, BS3 does not apply for functional assays assessed.
BP4
REVEL 0.33
PS3
This variant has not been functionally characterized to date.
PS2
To date, this variant has not been reported in the literature as de novo in an individual with a complex neurodevelopmental disorder.
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
To date, this variant has not been reported in the literature in an individual with a complex neurodevelopmental disorder.
PP3
REVEL 0.33
Curation History
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