chrM-608-A-G

Variant names:

• chrM-608-A-G
• rs387906735
• unassigned_transcript_4784:c.32A>G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000000000(TRNF):​c.32A>G​(p.His11Arg) variant causes a missense 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 0.0 (AC: 0)
• Consequence: TRNF ENST00000000000 missense
• Scores: Mitotip Uncertain 15
• Clinical Significance: Uncertain significance criteria provided, single submitter P:1 U:1 Tubulo-interstitial-nephritis
• Conservation: PhyloP100: 3.23
• Publications: 1 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very low frequency in mitomap database: 0.0

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRNF	unassigned_transcript_4784	c.32A>G	p.His11Arg	missense_variant	Exon 1 of 1
RNR1	unassigned_transcript_4785	n.-40A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT-TF	ENST00000387314.1	n.32A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
MT-RNR1	ENST00000389680.2	n.-40A>G		upstream_gene_variant		6

Frequencies

Mitomap GenBank AF: 0.0 AC: 0

Gnomad homoplasmic AF: 0.0 AC: 0 AN: 56426

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56426

Alfa AF: 0.00 Hom.: 0

Mitomap

Disease(s): Tubulo-interstitial-nephritis

Status: Reported

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:1 Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Interstitial nephritis Pathogenic:1

Mar 01, 2001

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

not specified Uncertain:1

May 04, 2022

Mendelics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mitotip	Uncertain	15
Hmtvar	Benign	0.30
PhyloP100		3.2

Other links and lift over

dbSNP: rs387906735; hg19: chrM-610;