M-15924-A-G

Position:

• chrM-15924-A-G

Variant summary

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

The ENST00000387460.2(MT-TT):​n.37A>G 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 0.035 (AC: 2140)
• Consequence: MT-TT ENST00000387460.2 non_coding_transcript_exon
• Scores: Mitotip Benign 8.0
• Clinical Significance: Benign criteria provided, single submitter B:1 LIMM
• Conservation: PhyloP100: -0.408

Genes affected

MT-TT (HGNC:7499): (mitochondrially encoded tRNA threonine)

TRNT (HGNC:):

MT-CYB (HGNC:7427): (mitochondrially encoded cytochrome b) Predicted to enable metal ion binding activity. Predicted to be involved in several processes, including electron transport coupled proton transport; response to cobalamin; and response to glucagon. Located in mitochondrion. Implicated in ovarian carcinoma and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]

MT-TP (HGNC:7494): (mitochondrially encoded tRNA proline)

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	TRNT.1	n.37A>G		non_coding_transcript_exon_variant	1/1
CYTB	CYTB.1			downstream_gene_variant			YP_003024038.1
TRNP	TRNP.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT-TT	ENST00000387460.2	n.37A>G		non_coding_transcript_exon_variant	1/1
MT-CYB	ENST00000361789.2			downstream_gene_variant				ENSP00000354554	P1
MT-TP	ENST00000387461.2			downstream_gene_variant

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

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.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;