chrM-477-T-C

Variant names:

• chrM-477-T-C
• rs41442247
• unassigned_transcript_4784:c.-100T>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000000000(TRNF):​c.-100T>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 0.0093 (AC: 567)
• Consequence: TRNF ENST00000000000 upstream_gene
• Clinical Significance: Not reported in ClinVar No linked disesase in Mitomap
• Conservation: PhyloP100: 0.415
• Publications: 4 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.

• BS1: High frequency in mitomap database: 0.0093
• BS2: High AC in GnomadMitoHomoplasmic at 867

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000387314.1. 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-TF	ENST00000387314.1	TSL:6	n.-100T>C		upstream_gene	N/A
	MT-RNR1	ENST00000389680.2	TSL:6	n.-171T>C		upstream_gene	N/A

Frequencies

Mitomap GenBank AF: 0.0093 AC: 567

Gnomad homoplasmic AF: 0.015 AC: 867 AN: 56431

Gnomad heteroplasmic AF: 0.000018 AC: 1 AN: 56431

Alfa AF: 0.000604 Hom.: 4

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.41

Other links and lift over

dbSNP: rs41442247; hg19: chrM-479;