rs3888511
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The ENST00000389680.2(MT-RNR1):n.314T>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 0.0091 ( AC: 555 )
Consequence
MT-RNR1
ENST00000389680.2 non_coding_transcript_exon
ENST00000389680.2 non_coding_transcript_exon
Scores
Clinical Significance
DEAF+-possibly-LVNC-associated,DEAF-/-AD-associated-/-intellectual-disability,Possibly-DEAF-associated
Conservation
PhyloP100: -7.53
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant M-961-T-C is Benign according to our data. Variant chrM-961-T-C is described in ClinVar as [Benign]. Clinvar id is 42236.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
High frequency in mitomap database: 0.0091
BS2
?
High AC in GnomadMitoHomoplasmic at 280
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNR1 | RNR1.1 use as main transcript | n.314T>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.314T>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:
555
Gnomad homoplasmic
AF:
AC:
280
AN:
56400
Gnomad heteroplasmic
AF:
AC:
18
AN:
56400
Alfa
AF:
Hom.:
Mitomap
DEAF+-possibly-LVNC-associated,DEAF-/-AD-associated-/-intellectual-disability,Possibly-DEAF-associated
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
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 | Dec 12, 2011 | 961T>C in MTRNR1: This variant is not expected to have clinical significance due to its presence at near equal frequencies in probands (4/1770) and control indi viduals (37/2662) (Li 2005, Tanaka 2004, Yao 2006, Lu 2010, http://www.mtdb.igp. uu.se). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at