M-5784-C-CT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate

Variant has been reported in ClinVar as Likely benign (★).

Frequency

Mitomap GenBank:
𝑓 0.0 ( AC: 2 )

Consequence

TRNC
frameshift

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1
No linked disesase in Mitomap

Conservation

PhyloP100: 0.390
Variant links:
Genes affected
TRNC (HGNC:7477): (mitochondrially encoded tRNA cysteine)
COX1 (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)
TRNW (HGNC:7501): (mitochondrially encoded tRNA tryptophan)
TRNY (HGNC:7502): (mitochondrially encoded tRNA tyrosine)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very low frequency in mitomap database: 0.0
BP6
Variant M-5784-C-CT is Benign according to our data. Variant chrM-5784-C-CT is described in ClinVar as [Likely_benign]. Clinvar id is 689990.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRNCunassigned_transcript_4797 c.42dupA p.Ala15fs frameshift_variant Exon 1 of 1
COX1unassigned_transcript_4799 c.-120_-119insT upstream_gene_variant
TRNNunassigned_transcript_4796 c.-56dupA upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.0
AC:
2

Mitomap

No disease associated.

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

MELAS syndrome Benign:1
Jul 12, 2019
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The NC_012920.1:m.5786dupT variant in MT-TC 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: BS4, BP6 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1603220115; hg19: chrM-5785; API