rs118203894

Variant names:

• chrM-5843-A-G
• rs118203894
• unassigned_transcript_4798:c.49T>C
• TRNY p.Leu17Leu

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP6_Moderate BP7 BS1 BS2

The ENST00000000000(TRNY):​c.49T>C​(p.Leu17Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.0074 (AC: 452)
• Consequence: TRNY ENST00000000000 synonymous
• Scores: Mitotip Benign 3.5
• Clinical Significance: Benign criteria provided, single submitter P:1 B:1 FSGS-/-Mitochondrial-Cytopathy
• Conservation: PhyloP100: 0.876
• Publications: 2 publications found

Genes affected

TRNY (HGNC:7502): (mitochondrially encoded tRNA tyrosine)

MT-CO1 (HGNC:7419): (mitochondrially encoded cytochrome c oxidase I) Contributes to cytochrome-c oxidase activity. Predicted to be involved in electron transport coupled proton transport and mitochondrial electron transport, cytochrome c to oxygen. Part of mitochondrial respiratory chain complex III and mitochondrial respiratory chain complex IV. [provided by Alliance of Genome Resources, Apr 2022]

TRNN (HGNC:7493): (mitochondrially encoded tRNA asparagine)

TRNA (HGNC:7475): (mitochondrially encoded tRNA alanine)

TRNC (HGNC:7477): (mitochondrially encoded tRNA cysteine)

TRNC Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: Mitochondrial Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP6: Variant M-5843-A-G is Benign according to our data. Variant chrM-5843-A-G is described in ClinVar as Benign. ClinVar VariationId is 9553.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.876 with no splicing effect.
• BS1: High frequency in mitomap database: 0.0074
• BS2: High AC in GnomadMitoHomoplasmic at 43

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000387409.1. 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-TY	ENST00000387409.1	TSL:6	n.49T>C		non_coding_transcript_exon	Exon 1 of 1
	MT-CO1	ENST00000361624.2	TSL:6	c.-61A>G		upstream_gene	N/A	ENSP00000354499.2	P00395
	MT-TA	ENST00000387392.1	TSL:6	n.-188T>C		upstream_gene	N/A

Frequencies

Mitomap GenBank AF: 0.0074 AC: 452

Gnomad homoplasmic AF: 0.00076 AC: 43 AN: 56422

Gnomad heteroplasmic AF: 0.000053 AC: 3 AN: 56422

Alfa AF: 0.000645 Hom.: 12

Mitomap

Disease(s): FSGS-/-Mitochondrial-Cytopathy

Status: Reported

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Focal segmental glomerulosclerosis and dilated cardiomyopathy (1)
-	-	1	MELAS syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
Mitotip	Benign	3.5
Hmtvar	Benign	0.30
PhyloP100		0.88

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

Other links and lift over

dbSNP: rs118203894;

hg19: chrM-5844;