rs28357984
Positions:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4BP6_ModerateBA1
The ENST00000361453.3(MT-ND2):c.709C>A(p.Leu237Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 7/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Mitomap GenBank:
𝑓 0.045 ( AC: 2752 )
Consequence
MT-ND2
ENST00000361453.3 missense
ENST00000361453.3 missense
Scores
Apogee2
Benign
Clinical Significance
Longevity-/-Extraversion-/-diabetes-/-AMS-protection-/-blood-iron-metabolism-/-correlation-with-myocardial-infarction-/-atherosclerosis
Conservation
PhyloP100: -4.27
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Apogee2 supports a benign effect, 0.03096441 < 0.5 .
BP6
Variant M-5178-C-A is Benign according to our data. Variant chrM-5178-C-A is described in ClinVar as [Benign]. Clinvar id is 692551.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
High frequency in mitomap database: 0.045
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-ND2 | ENST00000361453.3 | c.709C>A | p.Leu237Met | missense_variant | 1/1 | P1 |
Frequencies
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
AC:
2752
Gnomad homoplasmic
AF:
AC:
603
AN:
56426
Gnomad heteroplasmic
AF:
AC:
0
AN:
56426
Alfa
AF:
Hom.:
Mitomap
Longevity-/-Extraversion-/-diabetes-/-AMS-protection-/-blood-iron-metabolism-/-correlation-with-myocardial-infarction-/-atherosclerosis
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Leigh syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Oct 17, 2019 | The NC_012920.1:m.5178C>A (YP_003024027.1:p.Leu237Met) 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:
Name
Calibrated prediction
Score
Prediction
Apogee2
Benign
Hmtvar
Pathogenic
AlphaMissense
Benign
BayesDel_addAF
Benign
T
DEOGEN2
Benign
T
LIST_S2
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N
PROVEAN
Benign
N
GERP RS
Varity_R
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at