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.1571G>A (p.Arg524Gln)

CA1939839

464902 (ClinVar)

Gene: SCN2A
Condition: complex neurodevelopmental disorder
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: b4f59633-c8bf-471f-888f-87cad5a4bb36
Approved on: 2024-05-09
Published on: 2024-05-09

HGVS expressions

NM_001040142.2:c.1571G>A
NM_001040142.2(SCN2A):c.1571G>A (p.Arg524Gln)
NC_000002.12:g.165315658G>A
CM000664.2:g.165315658G>A
NC_000002.11:g.166172168G>A
CM000664.1:g.166172168G>A
NC_000002.10:g.165880414G>A
NG_008143.1:g.81257G>A
ENST00000631182.3:c.1571G>A
ENST00000375437.7:c.1571G>A
ENST00000635945.1:n.1934G>A
ENST00000636071.2:c.1571G>A
ENST00000636135.1:c.1442G>A
ENST00000636384.2:c.1571G>A
ENST00000636662.2:c.*2094G>A
ENST00000636769.1:c.1571G>A
ENST00000636985.2:c.1175G>A
ENST00000637266.2:c.1571G>A
ENST00000637367.1:c.*1504G>A
ENST00000638151.1:n.1655G>A
ENST00000283256.10:c.1571G>A
ENST00000375427.4:c.1571G>A
ENST00000375437.6:c.1571G>A
ENST00000480032.4:n.1714G>A
ENST00000631182.2:c.1571G>A
NM_001040142.1:c.1571G>A
NM_001040143.1:c.1571G>A
NM_021007.2:c.1571G>A
NM_001040143.2:c.1571G>A
NM_001371246.1:c.1571G>A
NM_001371247.1:c.1571G>A
NM_021007.3:c.1571G>A
More

Benign

Met criteria codes 2
BA1 BP4
Not Met criteria codes 10
PM2 PM1 PM5 BS3 BP1 PS3 PS1 PP1 PP3 PP2

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.1571G>A variant in SCN2A is a missense variant predicted to cause substitution of Arginine by Glutamine at amino acid 524 (p.Arg524Gln). The highest population minor allele frequency in gnomAD v2.1.1 is 0.1504% (30/19942 alleles) in Asian population, which is higher than the ClinGen Epilepsy Sodium Channel VCEP threshold (0.01%) for BA1, and therefore meets this criterion (BA1). The computational predictor REVEL gives a score of 0.192, evidence that does not predict a damaging effect on SCN2A function (BP4). 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 and BP4. (Version 1; approved 6/13/2023)
Met criteria codes
BA1
The highest population minor allele frequency in gnomAD v20210610 is 0.1504% (30/19942 alleles) in Asian population, which is higher than the ClinGen Epilepsy Sodium Channel VCEP threshold ( 0.01%) for BA1, and therefore meets this criterion (BA1).
BP4
The computational predictor REVEL gives a score of 0.192, evidence that does not predict a damaging effect on SCN2A function (BP4).
Not Met criteria codes
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
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
BS3
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
PS3
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
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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