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]
  • 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.12308A>G

CA337099441

690193 (ClinVar)

Gene: MT-TL2
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
Link to MONDO
UUID: a63828d3-9965-4256-95c2-c1579650125d
Approved on: 2022-01-10
Published on: 2022-01-10

HGVS expressions

NC_012920.1:m.12308A>G
J01415.2:m.12308A>G

Benign

Met criteria codes 1
BA1
Not Met criteria codes 2
PP3 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.12308A>G variant in MT-TL2 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). This variant is seen in 12.5% of individuals in the GenBank dataset (BA1) including in haplogroups K (99.5% of individuals) and U (98.9% of individuals). Furthermore, this variant is seen in the gnomAD dataset (v3.1.2) at an overall homoplasmic allele frequency of 15% including in haplogroups K (99.9% of individuals) and U (99.7% of individuals). If an affected individual is not a member one of these haplogroups, further evaluation of the variant in that particular individual should be considered. In summary, this variant meets criteria to be classified as benign 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: BA1.
Met criteria codes
BA1
This variant is seen in 12.5% of individuals in the GenBank dataset (BA1) including in haplogroups K (99.5% of individuals) and U (98.9% of individuals). Furthermore, this variant is seen in the gnomAD dataset (v3.1.2) at an overall homoplasmic allele frequency of 15% including in haplogroups K (99.9% of individuals) and U (99.7% of individuals). If an affected individual is not a member one of these haplogroups, further evaluation of the variant in that particular individual should be considered.
Not Met criteria codes
PP3
HmtVar: 0.4 - likely pathogenic; MitoTIP: possibly benign (42nd percentile)
BP4
HmtVar: 0.4 - likely pathogenic; MitoTIP: possibly benign (42nd percentile)
Curation History
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