chrM-10192-C-T

Position:

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM5BP4BP6_ModerateBS2

The ENST00000361227.2(MT-ND3):​c.134C>T​(p.Ser45Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S45P) has been classified as Pathogenic.

Frequency

Mitomap GenBank:
𝑓 0.0017 ( AC: 106 )

Consequence

MT-ND3
ENST00000361227.2 missense

Scores

Apogee2
Benign
0.32

Clinical Significance

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

Conservation

PhyloP100: 2.70
Variant links:
Genes affected
MT-ND3 (HGNC:7458): (mitochondrially encoded NADH dehydrogenase 3) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; Leigh disease; and Parkinson's disease. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM5
Other missense variant is known to change same aminoacid residue: Variant chrM-10191-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 9712.Status of the report is reviewed_by_expert_panel, 3 stars.
BP4
Apogee2 supports a benign effect, 0.31512925 < 0.5 .
BP6
Variant M-10192-C-T is Benign according to our data. Variant chrM-10192-C-T is described in ClinVar as [Benign]. Clinvar id is 693271.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomadMitoHomoplasmic at 81

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MT-ND3ENST00000361227.2 linkuse as main transcriptc.134C>T p.Ser45Phe missense_variant 1/1 ENSP00000355206 P1

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.0017
AC:
106
Gnomad homoplasmic
AF:
0.0014
AC:
81
AN:
56429
Gnomad heteroplasmic
AF:
0.000035
AC:
2
AN:
56429
Alfa
AF:
0.00110
Hom.:
9

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.10192C>T (YP_003024033.1:p.Ser45Phe) variant in MTND3 gene is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BS1, BS2, BP4 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Apogee2
Benign
0.32
Hmtvar
Benign
0.21
AlphaMissense
Uncertain
0.38
BayesDel_addAF
Benign
-0.28
T
DEOGEN2
Uncertain
0.63
D
LIST_S2
Benign
0.22
T
MutationAssessor
Uncertain
2.1
M
MutationTaster
Benign
1.0
N
PROVEAN
Uncertain
-3.5
D
Sift
Uncertain
0.021
D
Sift4G
Pathogenic
0.0
D
GERP RS
1.2
Varity_R
0.31

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: rs1556423776; hg19: chrM-10193; API