M-4561-T-C

Position:

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

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

Frequency

Mitomap GenBank:
𝑓 0.0063 ( AC: 386 )

Consequence

ND2
missense

Scores

Apogee2
Benign
0.050

Clinical Significance

Benign criteria provided, single submitter B:1
No linked disesase in Mitomap

Conservation

PhyloP100: 0.651
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant M-4561-T-C is Benign according to our data. Variant chrM-4561-T-C is described in ClinVar as [Benign]. Clinvar id is 692463.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
High frequency in mitomap database: 0.0063
BS2
High AC in GnomadMitoHomoplasmic at 486

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ND2unassigned_transcript_4793 c.92T>C p.Val31Ala missense_variant 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons 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:
0.0063
AC:
386
Gnomad homoplasmic
AF:
0.0086
AC:
486
AN:
56421
Gnomad heteroplasmic
AF:
0.000053
AC:
3
AN:
56421
Alfa
AF:
0.0288
Hom.:
126

Mitomap

No disease associated.

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 submitterclinical testingWong Mito Lab, Molecular and Human Genetics, Baylor College of MedicineOct 17, 2019The NC_012920.1:m.4561T>C (YP_003024027.1:p.Val31Ala) variant in MTND2 gene is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished).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
0.050
Hmtvar
Benign
0.14
AlphaMissense
Benign
0.17
BayesDel_addAF
Benign
-0.54
T
DEOGEN2
Benign
0.051
T
LIST_S2
Benign
0.41
T
MutationAssessor
Benign
0.10
N
PROVEAN
Benign
-2.2
N
Sift4G
Benign
0.22
T
GERP RS
2.5
Varity_R
0.12

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs41376350; hg19: chrM-4562; API