M-5875-C-T

Position:

• chrM-5875-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4 BP6_Moderate

The ENST00000387409.1(MT-TY):​n.17G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.00010 (AC: 5)
• Consequence: MT-TY ENST00000387409.1 non_coding_transcript_exon
• Scores: Mitotip Benign 2.9
• Clinical Significance: Likely benign criteria provided, single submitter B:1 No linked disesase in Mitomap
• Conservation: PhyloP100: -2.47

Genes affected

MT-TY (HGNC:7502): (mitochondrially encoded tRNA tyrosine)

TRNY (HGNC:):

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]

MT-TC (HGNC:7477): (mitochondrially encoded tRNA cysteine)

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• BP4: Mitotip and hmtvar scores support benign criterium.
• BP6: Variant M-5875-C-T is Benign according to our data. Variant chrM-5875-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 690022.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRNY	TRNY.1	n.17G>A		non_coding_transcript_exon_variant	1/1
COX1	COX1.1			upstream_gene_variant			YP_003024028.1
TRNC	TRNC.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT-TY	ENST00000387409.1	n.17G>A		non_coding_transcript_exon_variant	1/1
MT-CO1	ENST00000361624.2			upstream_gene_variant				ENSP00000354499	P1
MT-TC	ENST00000387405.1			upstream_gene_variant

Frequencies

GnomAD4 exome Cov.: 0

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

Mitomap GenBank AF: 0.00010 AC: 5

Gnomad homoplasmic AF: 0.000053 AC: 3 AN: 56433

Gnomad heteroplasmic AF: 0.000018 AC: 1 AN: 56433

Mitomap

No disease associated.

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Juvenile myopathy, encephalopathy, lactic acidosis AND stroke Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine

Jul 12, 2019

The NC_012920.1:m.5875C>T variant in MT-TY gene is interpreted to be a Likely Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: BS1, BP4, BP6 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mitotip	Benign	2.9
Hmtvar	Benign	0.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1603220162; hg19: chrM-5876;