chrM-14798-T-C
Position:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4BP6_ModerateBA1
The ENST00000361789.2(MT-CYB):āc.52T>Cā(p.Phe18Leu) variant causes a missense 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 Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Mitomap GenBank:
š 0.067 ( AC: 4089 )
Consequence
MT-CYB
ENST00000361789.2 missense
ENST00000361789.2 missense
Scores
Apogee2
Benign
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: -1.53
Genes affected
MT-CYB (HGNC:7427): (mitochondrially encoded cytochrome b) Predicted to enable metal ion binding activity. Predicted to be involved in several processes, including electron transport coupled proton transport; response to cobalamin; and response to glucagon. Located in mitochondrion. Implicated in ovarian carcinoma and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Apogee2 supports a benign effect, 0.0047416794 < 0.5 .
BP6
Variant M-14798-T-C is Benign according to our data. Variant chrM-14798-T-C is described in ClinVar as [Benign]. Clinvar id is 693768.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
High frequency in mitomap database: 0.0669
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYTB | CYTB.1 use as main transcript | c.52T>C | p.Phe18Leu | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-CYB | ENST00000361789.2 | c.52T>C | p.Phe18Leu | 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:
4089
Gnomad homoplasmic
AF:
AC:
4938
AN:
56360
Gnomad heteroplasmic
AF:
AC:
7
AN:
56360
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
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.14798T>C (YP_003024038.1:p.Phe18Leu) variant in MTCYB 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
Benign
AlphaMissense
Uncertain
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at