Genetic Variant TRNW:p.Ser13Ile (chrM-5549-G-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Mitomap GenBank:

Absent

Consequence

TRNW
missense

Scores

Mitotip

Pathogenic

Clinical Significance

Not reported in ClinVar

No linked disesase in Mitomap

Conservation

PhyloP100: 5.29

Variant links:

Genes affected

TRNW (HGNC:7501): (mitochondrially encoded tRNA tryptophan)

TRNW links:

ND2 (HGNC:7456): (mitochondrially encoded NADH dehydrogenase 2) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; multiple sclerosis; myocardial infarction; neurodegenerative disease (multiple); and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]

ND2 links:

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

TRNN links:

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

TRNA links:

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

TRNC links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

No frequency data in Mitomap. Probably very rare.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank
TRNW	unassigned_transcript_4794	c.38G>T	p.Ser13Ile	missense_variant	Exon 1 of 1
ND2	unassigned_transcript_4793	c.*38G>T		downstream_gene_variant
TRNN	unassigned_transcript_4796	c.*108C>A		downstream_gene_variant

Ensembl

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

Frequencies

GnomAD4 exome

Cov.:

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

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mitotip

Pathogenic

Hmtvar

Benign

0.050

Splicing

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

Publications

No publications associated with this variant yet.