Variant M-1654-TA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

Variant has been reported in ClinVar as Likely benign (★).

Frequency

Mitomap GenBank:

𝑓 0.00010 ( AC: 7 )

Consequence

TRNV
frameshift

Scores

Mitotip

Benign

2.5

Clinical Significance

Likely benign criteria provided, single submitter B:1

No linked disesase in Mitomap

Conservation

PhyloP100: -1.20

Variant links:

Genes affected

TRNV (HGNC:):

TRNV links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP6

Variant M-1654-TA-T is Benign according to our data. Variant chrM-1654-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 689849.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons
TRNV	unassigned_transcript_4787 use as main transcript	c.55delA	p.Thr19fs	frameshift_variant	1/1
RNR2	unassigned_transcript_4788 use as main transcript	n.-16delA		upstream_gene_variant
	use as main transcript

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

MELAS syndrome

Benign:1

Likely 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.1656delA variant in MT-TV gene is interpreted to be a Likely Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: BP4, BP6 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction