rs111033179

Variant names:

• chrM-1005-T-C
• rs111033179
• ENST00000389680.2:n.358T>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.358T>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 0.0044 (AC: 272)
• Consequence: MT-RNR1 ENST00000389680.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1 DEAF
• Conservation: PhyloP100: -2.63
• Publications: 5 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 -6 ACMG points.

• BP6: Variant M-1005-T-C is Benign according to our data. Variant chrM-1005-T-C is described in ClinVar as Benign. ClinVar VariationId is 42201.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomadMitoHomoplasmic at 78

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNR1	unassigned_transcript_4785	n.358T>C		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.358T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

Mitomap GenBank AF: 0.0044 AC: 272

Gnomad homoplasmic AF: 0.0014 AC: 78 AN: 56423

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56423

Alfa AF: 0.00159 Hom.: 65

Mitomap

Disease(s): DEAF

Status: Unclear

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Jun 11, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

m.1005T>C in MTRNR1: This variant has been identified in 3/128 (2.3%) Chinese pe diatric individuals with hearing loss, but there is no evidence that these indiv iduals had a maternal family history of hearing loss (Li Z 2005). In addition, t his variant has been reported to be a benign polymorphism on MitoMap (www.mitoma p.org) and has also been identified in 7/2703 individuals in the Human Mitochond rial Genome Database (www.genpat.uu.se/mtDB/). Six of the seven (86%) individual s who have ethnicity data from the Human Mitochondrial Genome Database (www.genp at.uu.se/mtDB/) are of Asian decent. No phenotypic information is available from this database. Furthermore, this variant has been associated with a specific ha plotype in the Chinese population (Kong 2004). In summary, we believe this data suggests that the 1005T>C variant is likely to be a benign variant in the Asian population without clinical significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.6

Other links and lift over

dbSNP: rs111033179; hg19: chrM-1007;