rs28357980

Variant names:

• chrM-4917-A-G
• rs28357980
• unassigned_transcript_4793:c.448A>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.051 (AC: 3102)
• Consequence: ND2 missense
• Scores: Apogee2 Benign 0.23
• Clinical Significance: Benign criteria provided, single submitter U:1 B:1 LHON-/-Insulin-Resistance-/-AMD-/-NRTI-PN
• Conservation: PhyloP100: 2.23

Genes affected

ND2 (HGNC:7456): (mitochondrially encoded NADH dehydrogenase 2) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; multiple sclerosis; myocardial infarction; neurodegenerative disease (multiple); and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant M-4917-A-G is Benign according to our data. Variant chrM-4917-A-G is described in ClinVar as [Benign]. Clinvar id is 9716.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: High frequency in mitomap database: 0.0507

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ND2	unassigned_transcript_4793	c.448A>G	p.Asn150Asp	missense_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD4 exome Cov.: 0

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

Mitomap GenBank AF: 0.051 AC: 3102

Gnomad homoplasmic AF: 0.058 AC: 3247 AN: 56429

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56429

Alfa AF: 0.0951 Hom.: 4073

Mitomap

LHON-/-Insulin-Resistance-/-AMD-/-NRTI-PN

ClinVar

Significance: Benign

Submissions summary: Uncertain:1 Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Leber optic atrophy Uncertain:1

Mar 02, 2013

OMIM

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Leigh syndrome Benign:1

Oct 17, 2019

Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The NC_012920.1:m.4917A>G (YP_003024027.1:p.Asn150Asp) variant in MTND2 gene is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BA1 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Apogee2	Benign	0.23
Hmtvar	Benign	0.27
AlphaMissense	Benign	0.080
BayesDel_addAF	Benign	-0.49	T
DEOGEN2	Benign	0.059	T
LIST_S2	Benign	0.69	T
MutationAssessor	Benign	1.7	L
PROVEAN	Uncertain	-3.9	D
Sift4G	Benign	0.077	T
GERP RS		0.15
Varity_R		0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs28357980; hg19: chrM-4918;