Variant chrM-12246-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4BP6_Moderate

The ENST00000387449.1(MT-TS2):n.40C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Mitomap GenBank:

𝑓 0.00020 ( AC: 15 )

Consequence

MT-TS2
ENST00000387449.1 non_coding_transcript_exon

Scores

Mitotip

Benign

2.4

Clinical Significance

Benign criteria provided, single submitter B:1

No linked disesase in Mitomap

Conservation

PhyloP100: -4.64

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 Likely_benign. Variant got -3 ACMG points.

BP4

Mitotip and hmtvar scores support benign criterium.

BP6

Variant M-12246-C-T is Benign according to our data. Variant chrM-12246-C-T is described in ClinVar as [Benign]. Clinvar id is 690172.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
TRNS2	TRNS2.1 use as main transcript	n.40C>T	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.40C>T	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:

0.00020

AC:

Gnomad homoplasmic

AF:

0.0

AC:

AN:

56434

Gnomad heteroplasmic

AF:

0.000035

AC:

AN:

56434

Mitomap

No disease associated.

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Juvenile myopathy, encephalopathy, lactic acidosis AND stroke

Benign:1

Benign, 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.12246C>T variant in MT-TS2 gene is interpreted to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: BS1, BS2, BP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mitotip

Benign

2.4

Hmtvar

Benign

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Mitomap

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over