dbSNP rs878853056: MT-ND2:p.Ala73Ala (chrM-4688-T-C) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP6_ModerateBP7BS1BS2

The ENST00000361453.3(MT-ND2):c.219T>C(p.Ala73Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Mitomap GenBank:

𝑓 0.0067 ( AC: 410 )

Consequence

MT-ND2
ENST00000361453.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

No linked disesase in Mitomap

Conservation

PhyloP100: -20.0

Publications

5 publications found

Variant links:

Genes affected

MT-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]

MT-ND2 links:

TRNM (HGNC:7492): (mitochondrially encoded tRNA methionine)

TRNM Gene-Disease associations (from GenCC):

mitochondrial disease
Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen

TRNM links:

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new If you want to explore the variant's impact on the transcript ENST00000361453.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP6

Variant M-4688-T-C is Benign according to our data. Variant chrM-4688-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 235516.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-20 with no splicing effect.

BS1

High frequency in mitomap database: 0.0067000003

BS2

High AC in GnomadMitoHomoplasmic at 325

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361453.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT-ND2	ENST00000361453.3	TSL:6	c.219T>C	p.Ala73Ala	synonymous	Exon 1 of 1	ENSP00000355046.4	P03891
	MT-TM	ENST00000387377.1	TSL:6	n.*219T>C		downstream_gene	N/A

Frequencies

Mitomap GenBank

AF:

0.0067

AC:

410

Gnomad homoplasmic

AF:

0.0058

AC:

325

AN:

56412

Gnomad heteroplasmic

AF:

0.00016

AC:

AN:

56412

Alfa

AF:

0.00671

Hom.:

Mitomap

No disease associated.

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-20

Mutation Taster

=96/4

polymorphism

(source)

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Mitomap

ClinVar

Computational scores

Publications

Other links and lift over