rs878853008
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Mitomap GenBank:
𝑓 0.00080 ( AC: 49 )
Consequence
ND1
missense
missense
Scores
Apogee2
Benign
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: 0.0660
Genes affected
ND1 (HGNC:7455): (mitochondrially encoded NADH dehydrogenase 1) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Located in mitochondrial membrane. Part of mitochondrial respiratory chain complex I. Implicated in several diseases, including MELAS syndrome; neurodegenerative disease (multiple); optic nerve disease (multiple); toxic shock syndrome; and type 2 diabetes mellitus. Biomarker of Alzheimer's disease; Parkinson's disease; and multiple sclerosis. [provided by Alliance of Genome Resources, Apr 2022]
TRNI (HGNC:7488): (mitochondrially encoded tRNA isoleucine)
TRNM (HGNC:7492): (mitochondrially encoded tRNA methionine)
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP6
Variant M-4219-G-A is Benign according to our data. Variant chrM-4219-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 235315.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomadMitoHomoplasmic at 57
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ND1 | unassigned_transcript_4789 | c.913G>A | p.Val305Ile | missense_variant | Exon 1 of 1 | |||
TRNI | unassigned_transcript_4790 | c.-44G>A | upstream_gene_variant | |||||
TRNM | unassigned_transcript_4792 | c.-183G>A | upstream_gene_variant | |||||
TRNQ | unassigned_transcript_4791 | c.*110C>T | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|
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:
49
Gnomad homoplasmic
AF:
AC:
57
AN:
56416
Gnomad heteroplasmic
AF:
AC:
3
AN:
56416
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Leigh syndrome Benign:1
Oct 17, 2019
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
The NC_012920.1:m.4219G>A (YP_003024026.1:p.Val305Ile) variant in MTND1 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 -
not provided Benign:1
Aug 12, 2015
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Apogee2
Benign
Hmtvar
Benign
AlphaMissense
Benign
BayesDel_addAF
Benign
T
DEOGEN2
Benign
T
LIST_S2
Benign
T
MutationAssessor
Benign
N
PROVEAN
Benign
N
Sift4G
Benign
T
GERP RS
Varity_R
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at