rs111033356
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The ENST00000389680.2(MT-RNR1):n.773T>C 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 0.0021 ( AC: 131 )
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: -0.923
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP6
?
Variant M-1420-T-C is Benign according to our data. Variant chrM-1420-T-C is described in ClinVar as [Benign]. Clinvar id is 42219.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomadMitoHomoplasmic at 199
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNR1 | RNR1.1 use as main transcript | n.773T>C | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-RNR1 | ENST00000389680.2 | n.773T>C | non_coding_transcript_exon_variant | 1/1 |
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:
131
Gnomad homoplasmic
AF:
AC:
199
AN:
56423
Gnomad heteroplasmic
AF:
AC:
3
AN:
56423
Mitomap
No disease associated.
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 26, 2017 | m.1420T>C in MTRNR1: This variant is not expected to have clinical significance because it has been identified in 12.1% (55/456) of the L1c haplogroup in MitoMa p (https://www.mitomap.org). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at