rs2001030
Variant names:
Variant summary
Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The ENST00000389680.2(MT-RNR1):n.791A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).
Frequency
Mitomap GenBank:
𝑓 0.95 ( AC: 58266 )
Consequence
MT-RNR1
ENST00000389680.2 non_coding_transcript_exon
ENST00000389680.2 non_coding_transcript_exon
Scores
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: 0.238
Publications
29 publications found
Genes affected
MT-RNR1 (HGNC:7470): (mitochondrially encoded 12S RNA) Enables DNA binding activity and DNA-binding transcription factor binding activity. Involved in several processes, including osteoblast proliferation; regulation of carbohydrate utilization; and regulation of phosphate metabolic process. Located in extracellular space; mitochondrion; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
TRNV (HGNC:7500): (mitochondrially encoded tRNA valine)
MT-RNR2 (HGNC:7471): (mitochondrially encoded 16S RNA) Enables G protein-coupled receptor binding activity; protein self-association; and receptor antagonist activity. Involved in several processes, including leukocyte chemotaxis; negative regulation of cell death; and negative regulation of neuroinflammatory response. Located in several cellular components, including mitochondrion; perinuclear region of cytoplasm; and sperm midpiece. [provided by Alliance of Genome Resources, Apr 2022]
MT-RNR2 Gene-Disease associations (from GenCC):
- mitochondrial diseaseInheritance: Mitochondrial Classification: LIMITED Submitted by: ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -16 ACMG points.
BP6
Variant M-1438-A-G is Benign according to our data. Variant chrM-1438-A-G is described in ClinVar as Benign. ClinVar VariationId is 42220.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
High frequency in mitomap database: 0.95309997
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| RNR1 | unassigned_transcript_4785 | n.791A>G | non_coding_transcript_exon_variant | Exon 1 of 1 | ||||
| TRNV | unassigned_transcript_4786 | c.-164A>G | upstream_gene_variant | |||||
| RNR2 | unassigned_transcript_4787 | n.-233A>G | upstream_gene_variant |
Ensembl
Frequencies
Mitomap GenBank
AF:
AC:
58266
Gnomad homoplasmic
AF:
AC:
53745
AN:
56213
Gnomad heteroplasmic
AF:
AC:
4
AN:
56213
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Benign
Submissions summary: Benign:2Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Feb 16, 2025
Laboratory of Genetics, Children's Clinical University Hospital Latvia
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Mar 08, 2012
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
This variant is found at a high frequency (>90%) in the general population. -
not provided Other:1
-
GenomeConnect, ClinGen
Significance:not provided
Review Status:no classification provided
Collection Method:phenotyping only
GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Publications
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