rs267606618

Variant names:

• chrM-1095-T-C
• rs267606618
• ENST00000389680.2:n.448T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000000000(RNR1):​n.448T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as drug response (★★★).

• Frequency: Mitomap GenBank: 𝑓 0.0011 (AC: 65)
• Consequence: RNR1 ENST00000000000 non_coding_transcript_exon
• Clinical Significance: drug response reviewed by expert panel P:4 U:1 O:4 SNHL
• Conservation: PhyloP100: 2.56
• Publications: 16 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 -4 ACMG points.

• BS2: High AC in GnomadMitoHomoplasmic at 21

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT-RNR1	ENST00000389680.2	TSL:6	n.448T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

Mitomap GenBank AF: 0.0011 AC: 65

Gnomad homoplasmic AF: 0.00037 AC: 21 AN: 56428

Gnomad heteroplasmic AF: 0.000018 AC: 1 AN: 56428

Mitomap

Disease(s): SNHL

Status: Unclear

ClinVar

ClinVar submissions

Significance: drug response

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
1	-	-	Aminoglycoside-induced deafness (1)
1	-	-	Auditory neuropathy (1)
1	-	-	Mitochondrial non-syndromic sensorineural hearing loss (1)
1	-	-	not provided (1)
-	1	-	not specified (1)
-	-	-	aminoglycoside antibacterials response - Toxicity (1)
-	-	-	gentamicin response - Toxicity (1)
-	-	-	kanamycin response - Toxicity (1)
-	-	-	streptomycin response - Toxicity (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.6

Other links and lift over

dbSNP: rs267606618; hg19: chrM-1097;