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 computed assertion could be determined for this classification!


Variant: NM_001005361.3(DNM2):c.8A>G (p.Asn3Ser)

CA16620725

424401 (ClinVar)

Gene: DNM2
Condition: centronuclear myopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 1db99dce-6085-4713-bacc-8b3c1a4eed3c
Approved on: 2024-08-07
Published on: 2024-10-01

HGVS expressions

NM_001005361.3:c.8A>G
NM_001005361.3(DNM2):c.8A>G (p.Asn3Ser)
NC_000019.10:g.10718250A>G
CM000681.2:g.10718250A>G
NC_000019.9:g.10828926A>G
CM000681.1:g.10828926A>G
NC_000019.8:g.10689926A>G
NG_008792.1:g.5172A>G
ENST00000682285.1:n.196A>G
ENST00000682524.1:n.196A>G
ENST00000683738.1:n.196A>G
ENST00000355667.11:c.8A>G
ENST00000389253.9:c.8A>G
ENST00000355667.10:c.8A>G
ENST00000359692.10:c.8A>G
ENST00000389253.8:c.8A>G
ENST00000408974.8:c.8A>G
ENST00000585892.5:c.8A>G
NM_001005360.2:c.8A>G
NM_001005361.2:c.8A>G
NM_001005362.2:c.8A>G
NM_001190716.1:c.8A>G
NM_004945.3:c.8A>G
NM_001190716.2:c.8A>G
NM_001005360.3:c.8A>G
NM_001005362.3:c.8A>G
NM_004945.4:c.8A>G
More

Benign

Met criteria codes 1
BA1
Not Met criteria codes 5
PM2 PP3 PP2 BS1 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Congenital Myopathies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for DNM2 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Congenital Myopathies VCEP
The c.8A>G variant in DNM2 is a missense variant predicted to cause substitution of asparagine by serine at amino acid 3. The highest population filtering allele frequency in gnomAD v4.1 is 0.00001190 (2/43076 alleles) in the Admixed American population, which is higher than the ClinGen Congenital Myopathies VCEP threshold (≥0.0000015) for BA1, and therefore meets this criterion (BA1). The computational predictor REVEL gives a score of 0.57, which is neither above nor below the thresholds predicting a damaging or benign impact on DNM2 function. DNM2, in which the variant was identified, is defined by the ClinGen Congenital Myopathies VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2, not applied for this variant due to high allele frequency). In summary, this variant meets the criteria to be classified as benign for autosomal dominant centronuclear myopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathies VCEP: BA1. (Congenital Myopathies VCEP specifications version 1; 8/7/24)
Met criteria codes
BA1
The highest population filtering allele frequency in gnomAD v4.1 is 0.00001190 (2/43076 alleles) in the Admixed American population, which is higher than the ClinGen Congenital Myopathies VCEP threshold (≥0.0000015) for BA1, and therefore meets this criterion (BA1).
Not Met criteria codes
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
The computational predictor REVEL gives a score of 0.57, which is neither above nor below the thresholds predicting a damaging or benign impact on DNM2 function.
PP2
DNM2, in which the variant was identified, is defined by the ClinGen Congenital Myopathies VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2, not applied for this variant due to high allele frequency).
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
The computational predictor REVEL gives a score of 0.57, which is neither above nor below the thresholds predicting a damaging or benign impact on DNM2 function.
Curation History
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