chrM-16188-C-G

Variant names:

• chrM-16188-C-G
• rs55749223
• unassigned_transcript_4820:c.-165G>C

Variant summary

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

The ENST00000000000(TRNP):​c.-165G>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 0.0090 (AC: 550)
• Consequence: TRNP ENST00000000000 upstream_gene
• Clinical Significance: Not reported in ClinVar No linked disesase in Mitomap
• Conservation: PhyloP100: -4.89
• Publications: 5 publications found

Genes affected

TRNP (HGNC:7494): (mitochondrially encoded tRNA proline)

TRNT (HGNC:7499): (mitochondrially encoded tRNA threonine)

TRNT Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: Mitochondrial Classification: MODERATE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: High frequency in mitomap database: 0.009
• BS2: High AC in GnomadMitoHomoplasmic at 25

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000387461.2. 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-TP	ENST00000387461.2	TSL:6	n.-165G>C		upstream_gene	N/A
	MT-TT	ENST00000387460.2	TSL:6	n.*235C>G		downstream_gene	N/A

Frequencies

Mitomap GenBank AF: 0.0090 AC: 550

Gnomad homoplasmic AF: 0.00044 AC: 25 AN: 56429

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56429

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-4.9

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs55749223;

hg19: chrM-16190;