rs386829057
Positions:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP6_ModerateBP7BS2
The ENST00000361899.2(MT-ATP6):c.360G>A(p.Lys120=) 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 0.00090 ( AC: 53 )
Consequence
MT-ATP6
ENST00000361899.2 synonymous
ENST00000361899.2 synonymous
Scores
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: 0.435
Genes affected
MT-ATP6 (HGNC:7414): (mitochondrially encoded ATP synthase 6) Contributes to proton-transporting ATP synthase activity, rotational mechanism. Involved in mitochondrial ATP synthesis coupled proton transport. Part of mitochondrial proton-transporting ATP synthase complex. Implicated in Leber hereditary optic neuropathy; NARP syndrome; Parkinson's disease; multiple sclerosis; and systemic lupus erythematosus. [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-8886-G-A is Benign according to our data. Variant chrM-8886-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 376933.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.435 with no splicing effect.
BS2
?
High AC in GnomadMitoHomoplasmic at 38
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| ATP6 | ATP6.1 use as main transcript | c.360G>A | p.Lys120= | synonymous_variant | 1/1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MT-ATP6 | ENST00000361899.2 | c.360G>A | p.Lys120= | 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:
53
Gnomad homoplasmic
AF:
AC:
38
AN:
56427
Gnomad heteroplasmic
AF:
AC:
0
AN:
56427
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 | Jan 24, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at