M-489-T-C

Variant names:

• chrM-489-T-C
• rs28625645
• unassigned_transcript_4784:c.-88T>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000000000(TRNF):​c.-88T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Mitomap GenBank: 𝑓 0.25 (AC: 15321)
• Consequence: TRNF ENST00000000000 upstream_gene
• Clinical Significance: Not reported in ClinVar No linked disesase in Mitomap
• Conservation: PhyloP100: -1.46
• Publications: 15 publications found

Genes affected

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

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: Benign. The variant received -8 ACMG points.

• BA1: High frequency in mitomap database: 0.25059998

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRNF	unassigned_transcript_4784	c.-88T>C		upstream_gene_variant
RNR1	unassigned_transcript_4785	n.-159T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT-TF	ENST00000387314.1	n.-88T>C		upstream_gene_variant		6
MT-RNR1	ENST00000389680.2	n.-159T>C		upstream_gene_variant		6

Frequencies

Mitomap GenBank AF: 0.25 AC: 15321

Gnomad homoplasmic AF: 0.11 AC: 6162 AN: 56350

Gnomad heteroplasmic AF: 0.000035 AC: 2 AN: 56350

Alfa AF: 0.0817 Hom.: 1676

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.5

Other links and lift over

dbSNP: rs28625645; hg19: chrM-491;