NC_012920.1:m.4769A>G AND Mitochondrial disease

Germline classification:: Benign (1 submission)
Last evaluated:: Mar 24, 2022
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002221548.1

Allele description [Variation Report for NC_012920.1:m.4769A>G]

NC_012920.1:m.4769A>G

Gene:

MT-ND2:mitochondrially encoded NADH dehydrogenase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Genomic location:

Preferred name:

NC_012920.1:m.4769A>G

HGVS:

NC_012920.1:m.4769A>G

Links:

dbSNP: rs3021086

NCBI 1000 Genomes Browser:

rs3021086

Condition(s)

Name:: Mitochondrial disease
Synonyms:: Mitochondrial diseases; Mitochondrial disorder
Identifiers:: MONDO: MONDO:0044970; MeSH: D028361; MedGen: C0751651; Orphanet: 68380

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002498778	ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel, ClinGen	reviewed by expert panel (clingen mito disease acmg specifications v1-1)	Benign (Mar 24, 2022)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002498778

ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel, ClinGen

reviewed by expert panel

(clingen mito disease acmg specifications v1-1)

Benign
(Mar 24, 2022)

germline

curation

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation

Details of each submission

From ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel, ClinGen, SCV002498778.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	not provided

Description

The m.4769A>G (p.M100M) variant in MT-ND2 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 at high frequencies in numerous haplogroups and the overall allele frequency in GenBank database (per Mitomap; queried 6/29/2020) is 97.6% (BA1). This is a synonymous variant (BP7). In summary, this variant meets criteria to be classified as benign given its synonymous nature and high frequency in the general population. 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, BP7.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 9, 2023

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