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 computed assertion could be determined for this classification!

Variant: NM_001164508.2(NEB):c.11067C>T (p.Asn3689=)

CA1908888

389787 (ClinVar)

Gene: NEB
Condition: nemaline myopathy
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: ab51755b-d658-49af-b1b1-9397a3bd02bf
Approved on: 2024-08-07
Published on: 2024-10-01

HGVS expressions

NM_001164508.2:c.11067C>T
NM_001164508.2(NEB):c.11067C>T (p.Asn3689=)
NC_000002.12:g.151618284G>A
CM000664.2:g.151618284G>A
NC_000002.11:g.152474798G>A
CM000664.1:g.152474798G>A
NC_000002.10:g.152183044G>A
NG_009382.2:g.121204C>T
ENST00000397345.8:c.11067C>T
ENST00000427231.7:c.11067C>T
ENST00000172853.14:c.10338C>T
ENST00000397345.7:c.11067C>T
ENST00000409198.5:c.10338C>T
ENST00000427231.6:c.11067C>T
ENST00000603639.5:c.11067C>T
ENST00000604864.5:c.11067C>T
ENST00000618972.4:c.11067C>T
NM_001164507.1:c.11067C>T
NM_001164508.1:c.11067C>T
NM_001271208.1:c.11067C>T
NM_004543.4:c.10338C>T
NM_001271208.2:c.11067C>T
NM_004543.5:c.10338C>T
NM_001164507.2:c.11067C>T
More

Likely Benign

Met criteria codes 3
BS1 BP7 BP4
Not Met criteria codes 3
BA1 PP3 PM2

Evidence Links 0

Expert Panel

Criteria Specification Information

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Congenital Myopathies VCEP
The c.11067C>T is a synonymous (silent) variant (p.Asn3689=) that is not predicted by SpliceAI to impact splicing. In addition, it occurs at a nucleotide that is not conserved as shown by the UCSC Genome Browser (BP4, BP7). The highest population filtering allele frequency in gnomAD v4.1.0 is 0.0006878 (922/1461502 alleles, 2 homozygotes) in the non-Finnish European population, which is higher than the ClinGen Congenital Myopathies VCEP threshold (MAF ≥ 0.000237) for BS1, and therefore meets this criterion (BS1). In summary, this variant meets the criteria to be classified as likely benign for autosomal recessive congenital myopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathy VCEP: BS1, BP4, BP7. (Congenital Myopathies VCEP specifications version 1; 8/7/2024)
Met criteria codes
BS1
The highest population filtering allele frequency in gnomAD v4.1.0 is 0.0006878 (922/1461502 alleles, 2 homozygotes) in the non-Finnish European population, which is higher than the ClinGen Congenital Myopathies VCEP threshold (MAF ≥ 0.000237) for BS1, and therefore meets this criterion (BS1).
BP7
The c.11067C>T (p.Asn3689=) is a silent variant that is not predicted by SpliceAI to impact splicing. In addition, it occurs at a nucleotide that is not conserved as shown by the UCSC Genome Browser
BP4
The c.11067C>T (p.Asn3689=) is a silent variant that is not predicted by SpliceAI to impact splicing. In addition, it occurs at a nucleotide that is not conserved as shown by the UCSC Genome Browser
Not Met criteria codes
BA1
The highest population filtering allele frequency in gnomAD v4.1.0 is 0.0006878 (922/1461502 alleles, 2 homozygotes) in the non-Finnish European population
PP3
The c.11067C>T (p.Asn3689=) is a silent variant that is not predicted by SpliceAI to impact splicing. In addition, it occurs at a nucleotide that is not conserved as shown by the UCSC Genome Browser
PM2
The highest population filtering allele frequency in gnomAD v4.1.0 is 0.0006878 (922/1461502 alleles, 2 homozygotes) in the non-Finnish European population
Curation History
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