Variant M-5839-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4BP6_ModerateBS2

The ENST00000387409.1(MT-TY):n.53G>A 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 0.0011 ( AC: 68 )

Consequence

MT-TY
ENST00000387409.1 non_coding_transcript_exon

Scores

Mitotip

Benign

2.8

Clinical Significance

Benign criteria provided, single submitter B:1

No linked disesase in Mitomap

Conservation

PhyloP100: -4.26

Variant links:

Genes affected

MT-TY (HGNC:7502): (mitochondrially encoded tRNA tyrosine)

MT-TY links:

TRNY (HGNC:):

TRNY links:

MT-TC (HGNC:7477): (mitochondrially encoded tRNA cysteine)

MT-TC links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Mitotip and hmtvar scores support benign criterium.

BP6

Variant M-5839-C-T is Benign according to our data. Variant chrM-5839-C-T is described in ClinVar as [Benign]. Clinvar id is 690011.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomadMitoHomoplasmic at 46

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRNY	TRNY.1 use as main transcript	n.53G>A		non_coding_transcript_exon_variant	1/1
TRNC	TRNC.1 use as main transcript			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT-TY	ENST00000387409.1 linkuse as main transcript	n.53G>A		non_coding_transcript_exon_variant	1/1
MT-TC	ENST00000387405.1 linkuse as main transcript			upstream_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:

0.0011

AC:

Gnomad homoplasmic

AF:

0.00082

AC:

AN:

56434

Gnomad heteroplasmic

AF:

0.0

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.5839C>T variant in MT-TY 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, BS4, BP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mitotip

Benign

2.8

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