Variant: NM_001005361.3(DNM2):c.162-6del

CA9200718

511239 (ClinVar)

Gene: DNM2

Condition: centronuclear myopathy

Inheritance Mode: Autosomal dominant inheritance

UUID: c60bc508-df8a-480f-ba8e-b48dc89d3efe

Approved on: 2024-08-07

Published on: 2024-10-01

HGVS expressions

NM_001005361.3:c.162-6del
NM_001005361.3(DNM2):c.162-6del
NC_000019.10:g.10759732del
CM000681.2:g.10759732del
NC_000019.9:g.10870408del
CM000681.1:g.10870408del
NC_000019.8:g.10731408del
NG_008792.1:g.46654del
ENST00000682285.1:n.350-6del
ENST00000682524.1:n.350-6del
ENST00000683738.1:n.350-6del
ENST00000355667.11:c.162-6del
ENST00000389253.9:c.162-6del
ENST00000355667.10:c.162-6del
ENST00000359692.10:c.162-6del
ENST00000389253.8:c.162-6del
ENST00000408974.8:c.162-6del
ENST00000585892.5:c.162-6del
ENST00000586939.5:c.-313-6del
ENST00000588976.1:n.467del
NM_001005360.2:c.162-6del
NM_001005361.2:c.162-6del
NM_001005362.2:c.162-6del
NM_001190716.1:c.162-6del
NM_004945.3:c.162-6del
NM_001190716.2:c.162-6del
NM_001005360.3:c.162-6del
NM_001005362.3:c.162-6del
NM_004945.4:c.162-6del

Benign

• Met criteria codes: BP7 BP4 BA1

• Not Met criteria codes: BS1 PM2

Expert Panel

Congenital Myopathies VCEP

Criteria Specification Information

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

Evidence submitted by expert panel

Congenital Myopathies VCEP

The variant NM_001005361.3:c.162-6del in DNM2 is an intronic deletion variant. The highest population filtering allele frequency in gnomAD v4.1 is 0.0001715 (15/60000 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 c.162-6del variant is an intronic variant that is not predicted by SpliceAI to impact splicing. In addition, it occurs at a nucleotide that is not conserved as shown by UCSC Genome Browser (BP4, BP7). 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, BP4, BP7. (ClinGen Congenital Myopathies VCEP specifications version 1; 8/7/2024)

Met criteria codes

• BP7: SpliceAI produced a value of 0.01 for acceptor loss, and 0.00 for donor loss and gain and acceptor gain, and therefore the variant is not predicted to impact splicing.
• BP4: SpliceAI produced a value of 0.01 for acceptor loss, and 0.00 for donor loss and gain and acceptor gain, and therefore the variant is not predicted to impact splicing.
• BA1: The highest population filtering allele frequency in gnomAD v4.1 is 0.0001715 (15/60000 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

• BS1: 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