rs387907318

Positions:

• chrM-15924-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

Variant has been reported in ClinVar as Benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.035 (AC: 2140)
• Consequence: TRNT missense
• Scores: Mitotip Benign 8.0
• Clinical Significance: Benign criteria provided, single submitter B:1 LIMM
• Conservation: PhyloP100: -0.408

Genes affected

TRNT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant M-15924-A-G is Benign according to our data. Variant chrM-15924-A-G is described in ClinVar as [Benign]. Clinvar id is 690236.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: High frequency in mitomap database: 0.035

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRNT	unassigned_transcript_4820	c.37A>G	p.Thr13Ala	missense_variant	1/1
CYTB	unassigned_transcript_4819	c.*37A>G		downstream_gene_variant
TRNP	unassigned_transcript_4821	c.*32T>C		downstream_gene_variant

Ensembl

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

Frequencies

GnomAD4 exome Cov.: 0

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

Mitomap GenBank AF: 0.035 AC: 2140

Gnomad homoplasmic AF: 0.041 AC: 2316 AN: 56287

Gnomad heteroplasmic AF: 0.00052 AC: 29 AN: 56287

Alfa AF: 0.0636 Hom.: 1265

Mitomap

LIMM

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

MELAS syndrome 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.15924A>G variant in MT-TT gene is interpreted to be a Benign variant based on the modified ACMG guidelines (unpublished).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: BA1, BP4 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mitotip	Benign	8.0
Hmtvar	Pathogenic	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs193303001; hg19: chrM-15925;