M-827-A-G

Variant names:

• chrM-827-A-G
• rs28358569
• unassigned_transcript_4785:n.180A>G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

Variant has been reported in ClinVar as drug response (★).

• Frequency: Mitomap GenBank: 𝑓 0.026 (AC: 1585)
• Consequence: RNR1 non_coding_transcript_exon
• Clinical Significance: drug response criteria provided, single submitter P:2 O:1 DEAF
• Conservation: PhyloP100: 4.81

Genes affected

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)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: High frequency in mitomap database: 0.025899999

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNR1	unassigned_transcript_4785	n.180A>G		non_coding_transcript_exon_variant	Exon 1 of 1
TRNF	unassigned_transcript_4784	c.*180A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD4 exome Cov.: 0

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

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

Mitomap

DEAF

ClinVar

Significance: drug response

Submissions summary: Pathogenic:2 Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

Mitochondrial non-syndromic sensorineural hearing loss Pathogenic:1

Apr 11, 2008

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Aminoglycoside-induced deafness Pathogenic:1

Apr 11, 2008

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Gentamicin response Other:1

Aug 01, 2018

Medical Genetics Summaries

Significance: drug response

Review Status: criteria provided, single submitter

Collection Method: curation

The m.827A>G variant has been associated with non-syndromic hearing loss, both with and without the use of aminoglycosides. Adverse effect: Gentamicin-induced hearing loss

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs28358569; hg19: chrM-829;