rs118203894

chrM-5843-A-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4 BP6_Moderate BS1 BS2

The ENST00000387409.1(MT-TY):n.49T>C variant causes a non coding transcript exon 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: MT-TY ENST00000387409.1 non_coding_transcript_exon
• Scores: Mitotip Benign 3.5
• Clinical Significance: Benign criteria provided, single submitter P:1 B:1 FSGS-/-Mitochondrial-Cytopathy
• Conservation: PhyloP100: 0.876

Genes affected

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

TRNY (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Mitotip and hmtvar scores support benign criterium.
• BP6: Variant M-5843-A-G is Benign according to our data. Variant chrM-5843-A-G is described in ClinVar as [Benign]. Clinvar id is 9553.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: High frequency in mitomap database: 0.0074
• BS2: High AC in GnomadMitoHomoplasmic at 43

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRNY	TRNY.1	n.49T>C		non_coding_transcript_exon_variant	1/1
TRNC	TRNC.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-TY	ENST00000387409.1	n.49T>C		non_coding_transcript_exon_variant	1/1
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: 0.0074 AC: 452

Gnomad homoplasmic AF: 0.00076 AC: 43 AN: 56422

Gnomad heteroplasmic AF: 0.000053 AC: 3 AN: 56422

Mitomap

FSGS-/-Mitochondrial-Cytopathy

ClinVar

Significance: Benign

Submissions summary: Pathogenic:1 Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Focal segmental glomerulosclerosis and dilated cardiomyopathy Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Dec 01, 2003

- -

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

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.5843A>G variant in MT-TY gene is interpreted to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: BS1, BS2, BP4 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mitotip	Benign	3.5
Hmtvar	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs118203894; hg19: chrM-5844;