Variant M-12283-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5

The ENST00000387456.1(MT-TL2):n.18G>A variant causes a non coding transcript exon change. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Mitomap GenBank:

Absent

Consequence

MT-TL2
ENST00000387456.1 non_coding_transcript_exon

Scores

Mitotip

Uncertain

Clinical Significance

Pathogenic no assertion criteria provided P:1

CPEO

Conservation

PhyloP100: 6.20

Variant links:

Genes affected

MT-TL2 (HGNC:7491): (mitochondrially encoded tRNA leucine 2 (CUN))

MT-TL2 links:

TRNL2 (HGNC:):

TRNL2 links:

MT-TS2 (HGNC:7498): (mitochondrially encoded tRNA serine 2 (AGU/C))

MT-TS2 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2

No frequency data in Mitomap. Probably very rare.

PP5

Variant M-12283-G-A is Pathogenic according to our data. Variant chrM-12283-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 430688.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRNL2	TRNL2.1 use as main transcript	n.18G>A		non_coding_transcript_exon_variant	1/1
TRNS2	TRNS2.1 use as main transcript			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-TL2	ENST00000387456.1 linkuse as main transcript	n.18G>A		non_coding_transcript_exon_variant	1/1
MT-TS2	ENST00000387449.1 linkuse as main transcript			downstream_gene_variant

Frequencies

GnomAD4 exome

Cov.:

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

Mitomap

CPEO

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Mitochondrial disease

Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Wellcome Centre for Mitochondrial Research, Newcastle University

May 22, 2017

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction