dbSNP rs1556423008: TRNW:p.Ter16Ter (chrM-5559-A-G) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP7

The ENST00000000000(TRNW):c.48A>G(p.Ter16Ter) variant causes a stop retained change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Mitomap GenBank:

𝑓 0.0 ( AC: 0 )

Consequence

TRNW
ENST00000000000 stop_retained

Scores

Mitotip

Uncertain

Clinical Significance

Uncertain significance criteria provided, single submitter U:1O:1

Leigh-Syndrome

Conservation

PhyloP100: 1.34

Publications

0 publications found

Variant links:

Genes affected

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

TRNW links:

MT-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]

MT-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 Gene-Disease associations (from GenCC):

mitochondrial disease
Inheritance: Mitochondrial Classification: LIMITED Submitted by: ClinGen

TRNC links:

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new If you want to explore the variant's impact on the transcript ENST00000000000, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2

Very low frequency in mitomap database: 0.0

BP7

Synonymous conserved (PhyloP=1.34 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000387382.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MT-TW	ENST00000387382.1	TSL:6	n.48A>G	non_coding_transcript_exon	Exon 1 of 1
MT-ND2	ENST00000361453.3	TSL:6	c.*48A>G	downstream_gene	N/A	ENSP00000355046.4	P03891
MT-TA	ENST00000387392.1	TSL:6	n.*28T>C	downstream_gene	N/A

Frequencies

Mitomap GenBank

AF:

0.0

AC:

Gnomad homoplasmic

AF:

0.0

AC:

AN:

56427

Gnomad heteroplasmic

AF:

0.000018

AC:

AN:

56427

Alfa

AF:

0.00122

Hom.:

Mitomap

Disease(s): Leigh-Syndrome

Status: Reported

Publication(s):

31965079

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

MELAS syndrome (1)

Leigh syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

Mitotip

Uncertain

Hmtvar

Benign

0.25

PhyloP100

1.3

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Mitomap

ClinVar

Computational scores

Publications

Other links and lift over