The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document
  • ClinVar Id was derived from the Allele Registry.
  • There was no gene found in the curated document received from the VCI/VCEP
  • Gene listed was thus derived from ClinVar and/or CAR

  • See Evidence submitted by expert panel for details.

Variant: NC_012920.1:m.5558A>G

CA414780655

689941 (ClinVar)

Gene: MT-TW
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 508eef73-f9bd-414b-b7d0-7af3b73be5d2

HGVS expressions

NC_012920.1:m.5558A>G
J01415.2:m.5558A>G

Uncertain Significance

Met criteria codes 1
BP4
Not Met criteria codes 7
BS1 PS3 PS4 BA1 PP1 PP3 PM2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.5558A>G variant in MT-TW was reviewed by the Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel as part of the variant pilot for mitochondrial DNA variant specifications (McCormick et al., 2020; PMID: 32906214). There have been no affected individuals reported in the medical literature to our knowledge. There are no large families reported in the medical literature to consider for evidence of segregation. There are over 100 occurrences in MITOMAP for an overall allele frequency of 0.2%. This does not meet criteria for BA1 or BS1. The computational predictor MitoTIP suggests this variant is possibly benign (31st percentile) and HmtVAR predicts it to be likely polymorphic (0.5, BP4). There are no cybrid or single fiber studies reported on this variant. In summary, this variant meets criteria to be classified as uncertain significance for primary mitochondrial disease inherited in a mitochondrial manner. This classification was approved by the NICHD U24 Mitochondrial Disease Variant Curation Expert Panel as of August 20, 2020. Mitochondrial DNA-specific ACMG/AMP criteria applied: BP4.
Met criteria codes
BP4
MitoTIP: possibly benign (31st percentile); HmtVAR: likely polymorphic (0.5)
Not Met criteria codes
BS1
There are over 100 occurrences in MITOMAP for an overall allele frequency of 0.19%. This does not meet criteria for BA1 or BS1. Associated with haplogroups M6a (100% of individuals - 21/21), L0a (7.5% of individuals), H80 (2/5 individuals), T1a (11/551) - *If individual in whom this variant was identified is a member of a different haplogroup, consider further evaluation of this variant.* Allele frequency in GenBank database (per Mitomap, queried 6/29/2020) is 0.2%.
PS3
There are no cybrid or single fiber studies reported on this variant.
PS4
There have been no affected individuals reported in the medical literature to our knowledge.
BA1
There are over 100 occurrences in MITOMAP for an overall allele frequency of 0.19%. This does not meet criteria for BA1 or BS1.
PP1
There are no large families reported in the medical literature to consider for evidence of segregation.
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
There are over 100 occurrences in MITOMAP for an overall allele frequency of 0.2%. This does not meet criteria for BA1 or BS1.
Approved on: 2021-12-10
Published on: 2021-12-10
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