M-489-T-C

Variant names:

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

Variant summary

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

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

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

Genes affected

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

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]

ACMG classification

Verdict is Benign. Variant got -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

Frequencies

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

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

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: 0.100 Hom.: 1071

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

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: rs28625645; hg19: chrM-491;