chrM-951-G-A
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The ENST00000389680.2(MT-RNR1):n.304G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Mitomap GenBank:
𝑓 0.0072 ( AC: 440 )
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: 0.114
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-951-G-A is Benign according to our data. Variant chrM-951-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 42231.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
High frequency in mitomap database: 0.0072000003
BS2
High AC in GnomadMitoHomoplasmic at 426
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNR1 | RNR1.1 use as main transcript | n.304G>A | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-RNR1 | ENST00000389680.2 | n.304G>A | 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:
440
Gnomad homoplasmic
AF:
AC:
426
AN:
56426
Gnomad heteroplasmic
AF:
AC:
1
AN:
56426
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 28, 2013 | m.951G>A in MTRNR1: This variant is reported with low frequency, 0.1-4%, in broa d populations (LOVD database http://www.lovd.nl/2.0; mtDB http://www.mtdb.igp.uu .se; HmtDB http://www.hmtdb.uniba.it:8080/hmdb) and belongs to the H2a mitochond rial haplogroup (Brandstatter 2006). It has been identified in patients with hea ring loss (0.4 ? 1.6%) as well as in controls (0.4 - 1%) without a statistically significant difference (Konings 2008, Li_2004, Lu 2010, Rydzanicz 2010). In sum mary, in the absence of any statistically significant association to hearing los s, the frequency of this variant suggests that it is likely benign. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at