ENST00000389680.2:n.180A>G

Variant names:

• chrM-827-A-G
• rs28358569
• ENST00000389680.2:n.180A>G

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The ENST00000389680.2(MT-RNR1):​n.180A>G variant causes a non coding transcript exon change. Variant has been reported in ClinVar as Benign,drug response (★★).

• Frequency: Mitomap GenBank: 𝑓 0.026 (AC: 1585)
• Consequence: MT-RNR1 ENST00000389680.2 non_coding_transcript_exon
• Clinical Significance: Benign; drug response criteria provided, multiple submitters, no conflicts P:2 B:1 O:1 DEAF
• Conservation: PhyloP100: 4.81
• Publications: 10 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]

TRNF (HGNC:7481): (mitochondrially encoded tRNA phenylalanine)

TRNF Gene-Disease associations (from GenCC):

• mitochondrial disease

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

  Inheritance: Mitochondrial Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -16 ACMG points.

• BP6: Variant M-827-A-G is Benign according to our data. Variant chrM-827-A-G is described in ClinVar as Benign|drug_response. ClinVar VariationId is 9634.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: High frequency in mitomap database: 0.025899999

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.180A>G		non_coding_transcript_exon	Exon 1 of 1
	MT-TF	ENST00000387314.1	TSL:6	n.*180A>G		downstream_gene	N/A

Frequencies

Mitomap GenBank AF: 0.026 AC: 1585

Gnomad homoplasmic AF: 0.023 AC: 1309 AN: 56404

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56404

Alfa AF: 0.0296 Hom.: 347

Mitomap

Disease(s): DEAF

Status: Conflicting-reports

ClinVar

ClinVar submissions as Germline

Significance: Benign; drug response

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
1	-	1	Mitochondrial non-syndromic sensorineural hearing loss (2)
1	-	-	Aminoglycoside-induced deafness (1)
-	-	-	Gentamicin response (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.8
Mutation Taster		=65/35	polymorphism

Other links and lift over

dbSNP: rs28358569; hg19: chrM-829;