chrM-14783-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP6_ModerateBP7BA1
The ENST00000361789.2(MT-CYB):c.37T>C(p.Leu13=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Mitomap GenBank:
𝑓 0.20 ( AC: 12413 )
Consequence
MT-CYB
ENST00000361789.2 synonymous
ENST00000361789.2 synonymous
Scores
Clinical Significance
Possible-role-in-high-altitude-sickness
Conservation
PhyloP100: 3.18
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP6
?
Variant M-14783-T-C is Benign according to our data. Variant chrM-14783-T-C is described in ClinVar as [Benign]. Clinvar id is 140588.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=3.18 with no splicing effect.
BA1
?
High frequency in mitomap database: 0.203
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYTB | CYTB.1 use as main transcript | c.37T>C | p.Leu13= | synonymous_variant | 1/1 | ||
TRNE | TRNE.1 use as main transcript | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-CYB | ENST00000361789.2 | c.37T>C | p.Leu13= | synonymous_variant | 1/1 | P1 | |||
MT-TE | ENST00000387459.1 | upstream_gene_variant |
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:
12413
Gnomad homoplasmic
AF:
AC:
3118
AN:
56336
Gnomad heteroplasmic
AF:
AC:
3
AN:
56336
Alfa
AF:
Hom.:
Mitomap
Possible-role-in-high-altitude-sickness
ClinVar
Significance: Benign
Submissions summary: Pathogenic:1Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Familial cancer of breast Pathogenic:1Benign:1
Likely pathogenic, no assertion criteria provided | literature only | Department of Zoology Govt. MVM College | - | - - |
Benign, criteria provided, single submitter | curation | Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel | Aug 29, 2023 | Clinical significance based on ACMG v2.0 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at