rs1057516071
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The ENST00000361789.2(MT-CYB):c.108C>T(p.Leu36=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Mitomap GenBank:
𝑓 0.00020 ( AC: 10 )
Consequence
MT-CYB
ENST00000361789.2 synonymous
ENST00000361789.2 synonymous
Scores
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: -13.9
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 Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomadMitoHomoplasmic at 12
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CYTB | CYTB.1 use as main transcript | c.108C>T | p.Leu36= | synonymous_variant | 1/1 | YP_003024038.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MT-CYB | ENST00000361789.2 | c.108C>T | p.Leu36= | synonymous_variant | 1/1 | ENSP00000354554 | 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:
10
Gnomad homoplasmic
AF:
AC:
12
AN:
56433
Gnomad heteroplasmic
AF:
AC:
0
AN:
56433
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Mitochondrial cytopathy Uncertain:1
| Uncertain significance, no assertion criteria provided | clinical testing | Center for Neuroscience and Cell Biology, University of Coimbra, Portugal | Nov 21, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at