Variant M-12236-G-GC details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000387449.1(MT-TS2):n.35dup variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Mitomap GenBank:

𝑓 0.00010 ( AC: 6 )

Consequence

MT-TS2
ENST00000387449.1 non_coding_transcript_exon

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

No linked disesase in Mitomap

Conservation

PhyloP100: -4.19

Variant links:

Genes affected

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

MT-TS2 links:

TRNS2 (HGNC:):

TRNS2 links:

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

MT-TL2 links:

MT-TH (HGNC:7487): (mitochondrially encoded tRNA histidine)

MT-TH links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
TRNS2	TRNS2.1 use as main transcript	n.35dup	non_coding_transcript_exon_variant	1/1
TRNL2	TRNL2.1 use as main transcript		upstream_gene_variant
TRNH	TRNH.1 use as main transcript		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons
MT-TS2	ENST00000387449.1 linkuse as main transcript	n.35dup	non_coding_transcript_exon_variant	1/1
MT-TL2	ENST00000387456.1 linkuse as main transcript		upstream_gene_variant
MT-TH	ENST00000387441.1 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 GenBank

AF:

0.00010

AC:

Mitomap

No disease associated.

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Juvenile myopathy, encephalopathy, lactic acidosis AND stroke

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine

Jul 12, 2019

The NC_012920.1:m.12241dupC variant in MT-TS2 gene is interpreted to be a Unknown Significance variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: 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.