rs118203886

Variant names:

• chrM-611-G-A
• rs118203886
• unassigned_transcript_4784:c.35G>A

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PP5

The ENST00000000000(TRNF):​c.35G>A​(p.Trp12*) variant causes a stop gained change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Mitomap GenBank: Absent
• Consequence: TRNF ENST00000000000 stop_gained
• Scores: Mitotip Uncertain 13
• Clinical Significance: Pathogenic no assertion criteria provided P:1 O:1 MERRF
• Conservation: PhyloP100: 9.15
• Publications: 2 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 3 ACMG points.

• PM2: No frequency data in Mitomap. Probably very rare.
• PP5: Variant M-611-G-A is Pathogenic according to our data. Variant chrM-611-G-A is described in ClinVar as Pathogenic. ClinVar VariationId is 9574.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRNF	unassigned_transcript_4784	c.35G>A	p.Trp12*	stop_gained	Exon 1 of 1
RNR1	unassigned_transcript_4785	n.-37G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT-TF	ENST00000387314.1	n.35G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
MT-RNR1	ENST00000389680.2	n.-37G>A		upstream_gene_variant		6

Frequencies

Mitomap GenBank The variant is not present, suggesting it is rare .

Alfa AF: 0.00 Hom.: 0

Mitomap

Disease(s): MERRF

Status: Reported

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1 Other:1

Revision: no assertion criteria provided

Submissions by phenotype

MERRF syndrome Pathogenic:1 Other:1

Sep 25, 2007

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

-

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mitotip	Uncertain	13
Hmtvar	Pathogenic	0.85
PhyloP100		9.1

Other links and lift over

dbSNP: rs118203886; hg19: chrM-613;