rs201262114
Positions:
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4BP6_Very_StrongBS1BS2
The ENST00000361624.2(MT-CO1):c.358G>A(p.Ala120Thr) variant causes a missense change involving the alteration of a 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 0.0081 ( AC: 496 )
Consequence
MT-CO1
ENST00000361624.2 missense
ENST00000361624.2 missense
Scores
Apogee2
Benign
Clinical Significance
Prostate-Cancer-/-LHON
Conservation
PhyloP100: 7.69
Genes affected
MT-CO1 (HGNC:7419): (mitochondrially encoded cytochrome c oxidase I) Contributes to cytochrome-c oxidase activity. Predicted to be involved in electron transport coupled proton transport and mitochondrial electron transport, cytochrome c to oxygen. Part of mitochondrial respiratory chain complex III and mitochondrial respiratory chain complex IV. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Apogee2 supports a benign effect, 0.09348247 < 0.5 .
BP6
?
Variant M-6261-G-A is Benign according to our data. Variant chrM-6261-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 235718.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
High frequency in mitomap database: 0.0081
BS2
?
High AC in GnomadMitoHomoplasmic at 401
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COX1 | COX1.1 use as main transcript | c.358G>A | p.Ala120Thr | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-CO1 | ENST00000361624.2 | c.358G>A | p.Ala120Thr | missense_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:
496
Gnomad homoplasmic
AF:
AC:
401
AN:
56365
Gnomad heteroplasmic
AF:
AC:
10
AN:
56365
Alfa
AF:
Hom.:
Mitomap
Prostate-Cancer-/-LHON
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 15, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 16, 2019 | - - |
Leigh syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Oct 17, 2019 | The NC_012920.1:m.6261G>A (YP_003024028.1:p.Ala120Thr) variant in MTCO1 gene is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BA1 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Apogee2
Benign
Hmtvar
Pathogenic
AlphaMissense
Benign
BayesDel_addAF
Benign
T
DEOGEN2
Benign
T
LIST_S2
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
D
PROVEAN
Benign
N
Sift4G
Benign
T
GERP RS
Varity_R
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at