dbSNP rs3902405: MT-ND2:p.Leu332Leu (chrM-5465-T-C) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP6_ModerateBP7BA1

The ENST00000361453.3(MT-ND2):c.996T>C(p.Leu332Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Mitomap GenBank:

𝑓 0.038 ( AC: 2310 )

Consequence

MT-ND2
ENST00000361453.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

No linked disesase in Mitomap

Conservation

PhyloP100: -7.03

Publications

7 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:

TRNW (HGNC:7501): (mitochondrially encoded tRNA tryptophan)

TRNW links:

TRNN (HGNC:7493): (mitochondrially encoded tRNA asparagine)

TRNN links:

TRNA (HGNC:7475): (mitochondrially encoded tRNA alanine)

TRNA Gene-Disease associations (from GenCC):

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

TRNA 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-5465-T-C is Benign according to our data. Variant chrM-5465-T-C is described in ClinVar as Benign. ClinVar VariationId is 235745.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-7.03 with no splicing effect.

BA1

High frequency in mitomap database: 0.0378

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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MT-ND2	ENST00000361453.3	TSL:6	c.996T>C	p.Leu332Leu	synonymous	Exon 1 of 1	ENSP00000355046.4	P03891
MT-TW	ENST00000387382.1	TSL:6	n.-47T>C		upstream_gene	N/A
MT-TA	ENST00000387392.1	TSL:6	n.*122A>G		downstream_gene	N/A

Frequencies

Mitomap GenBank

AF:

0.038

AC:

2310

Gnomad homoplasmic

AF:

0.0032

AC:

178

AN:

56431

Gnomad heteroplasmic

AF:

0.000035

AC:

AN:

56431

Alfa

AF:

0.00273

Hom.:

Mitomap

No disease associated.

ClinVar

ClinVar submissions

Significance: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

-7.0

Mutation Taster

=97/3

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