chrM-5549-G-A

Position:

• chrM-5549-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Mitomap GenBank: Absent
• Consequence: TRNW missense
• Scores: Mitotip Pathogenic 17
• Clinical Significance: Pathogenic no assertion criteria provided P:1 DEMCHO-/-mitochondrial-encephalomyopathy
• Conservation: PhyloP100: 5.29

Genes affected

TRNW (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: No frequency data in Mitomap. Probably very rare.
• PP5: Variant M-5549-G-A is Pathogenic according to our data. Variant chrM-5549-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 9554.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRNW	unassigned_transcript_4795	c.38G>A	p.Ser13Asn	missense_variant	1/1
ND2	unassigned_transcript_4794	c.*38G>A		downstream_gene_variant
TRNA	unassigned_transcript_4796	c.*38C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

DEMCHO-/-mitochondrial-encephalomyopathy

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Mitochondrial encephalopathy Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 01, 1995

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mitotip	Pathogenic	17
Hmtvar	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs199474671; hg19: chrM-5550; COSMIC: COSV104419736;