chrM-3843-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP6_ModerateBP7BS2
The ENST00000361390.2(MT-ND1):c.537A>G(p.Trp179=) variant causes a synonymous 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 Likely benign (★).
Frequency
Mitomap GenBank:
𝑓 0.0035 ( AC: 214 )
Consequence
MT-ND1
ENST00000361390.2 synonymous
ENST00000361390.2 synonymous
Scores
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: 0.691
Genes affected
MT-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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP6
?
Variant M-3843-A-G is Benign according to our data. Variant chrM-3843-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 235228.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.691 with no splicing effect.
BS2
?
High AC in GnomadMitoHomoplasmic at 503
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-ND1 | ENST00000361390.2 | c.537A>G | p.Trp179= | synonymous_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:
214
Gnomad homoplasmic
AF:
AC:
503
AN:
56426
Gnomad heteroplasmic
AF:
AC:
4
AN:
56426
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 12, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
MutationTaster
Benign
N
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at