chrM-1382-A-C

Variant names:

• chrM-1382-A-C
• rs111033358
• ENST00000389680.2:n.735A>C

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The ENST00000389680.2(MT-RNR1):​n.735A>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 0.0031 (AC: 192)
• Consequence: MT-RNR1 ENST00000389680.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1 Longevity-/-T2D-susceptibility
• Conservation: PhyloP100: 2.13
• Publications: 14 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)

TRNV Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen
• Leigh syndrome

  Inheritance: Mitochondrial Classification: MODERATE Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP6: Variant M-1382-A-C is Benign according to our data. Variant chrM-1382-A-C is described in ClinVar as Benign. ClinVar VariationId is 42214.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomadMitoHomoplasmic at 37

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000389680.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT-RNR1	ENST00000389680.2	TSL:6	n.735A>C		non_coding_transcript_exon	Exon 1 of 1
	MT-TV	ENST00000387342.1	TSL:6	n.-220A>C		upstream_gene	N/A

Frequencies

Mitomap GenBank AF: 0.0031 AC: 192

Gnomad homoplasmic AF: 0.00066 AC: 37 AN: 56434

Gnomad heteroplasmic AF: 0.0 AC: 0 AN: 56434

Alfa AF: 0.00142 Hom.: 59

Mitomap

Disease(s): Longevity-/-T2D-susceptibility

Status: Reported

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Sep 26, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

m.1120C>T in MTRNR1: This variant is not expected to have clinical significance because it has been found in the general population at a frequency of 0.5% (122/ 24187 human mitochondrial DNA sequences) with a haplogroup-specific frequency of 2.1% and 69.1% in two different Japanese clades (http://www.mitomap.org). Addit ionally, this variant is not significantly over represented in individuals with nonsyndromic hearing loss as it has been found in 43/1642 (2.6%) Chinese childre n (a proportion of whom have been exposed to aminoglycosides) as well as 9/449 ( 2.0%) Chinese controls (Lu 2010), suggesting that this variant is most likely no t involved in the observed hearing loss.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.1

Other links and lift over

dbSNP: rs111033358; hg19: chrM-1384;