M-13212-C-T
Position:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP6_ModerateBP7BS2
The ENST00000361567.2(MT-ND5):c.876C>T(p.Ala292=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Mitomap GenBank:
𝑓 0.0012 ( AC: 75 )
Consequence
MT-ND5
ENST00000361567.2 synonymous
ENST00000361567.2 synonymous
Scores
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: -11.3
Genes affected
MT-ND5 (HGNC:7461): (mitochondrially encoded NADH dehydrogenase 5) 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; Leigh disease; and MELAS syndrome. [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-13212-C-T is Benign according to our data. Variant chrM-13212-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 445987.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-11.3 with no splicing effect.
BS2
High AC in GnomadMitoHomoplasmic at 39
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MT-ND5 | ENST00000361567.2 | c.876C>T | p.Ala292= | 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:
75
Gnomad homoplasmic
AF:
AC:
39
AN:
56434
Gnomad heteroplasmic
AF:
AC:
1
AN:
56434
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 | Jun 02, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at