ENST00000389680.2:n.311_313dupCCC

Variant names:

• chrM-955-A-ACCC
• rs111033185
• ENST00000389680.2:n.311_313dupCCC

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The ENST00000389680.2(MT-RNR1):​n.311_313dupCCC 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 0.00040 (AC: 27)
• Consequence: MT-RNR1 ENST00000389680.2 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1 No linked disesase in Mitomap
• Conservation: PhyloP100: -5.51
• Publications: 3 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]

MT-RNR1 Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP6: Variant M-955-A-ACCC is Benign according to our data. Variant chrM-955-A-ACCC is described in ClinVar as [Likely_benign]. Clinvar id is 42233.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNR1	unassigned_transcript_4785	n.311_313dupCCC		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT-RNR1	ENST00000389680.2	n.311_313dupCCC		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

Mitomap GenBank AF: 0.00040 AC: 27

Mitomap

No disease associated.

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Apr 18, 2018

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

m.958_960dupCCC in MTRNR1: This variant leads to the insertion of three cytosine nucleotides after position 960. Variable numbers of inserted Cs in this region have been putatively implicated in aminoglycoside-induced hearing loss (Casano 1 999, Yoshida 2002, Ronghua 2004). However, subsequent studies have revealed that these variants are present in similar frequencies among HL patients and control s and they are part of a common Asian haplogroup (Yao 2006, Bae 2008, Tanaka 201 0, Shen 2011). Moreover, this region of mitochondrial DNA is not evolutionarily conserved and its function is not well defined (Guan 2011). In summary, there is insufficient data to support a disease-associated role or risk for ototoxicity and the population frequency of the variant suggests that it is most likely beni gn. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-5.5

Other links and lift over

dbSNP: rs111033185; hg19: chrM-957;