chrM-15812-G-A

Variant names:

• chrM-15812-G-A
• rs200336777
• ENST00000361789.2:c.1066G>A

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4 BP6_Moderate BS1 BS2

The ENST00000361789.2(MT-CYB):​c.1066G>A​(p.Val356Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V356A) has been classified as Benign.

• Frequency: Mitomap GenBank: 𝑓 0.0084 (AC: 513)
• Consequence: MT-CYB ENST00000361789.2 missense
• Scores: Apogee2 Benign 0.098
• Clinical Significance: Benign criteria provided, single submitter P:1 B:1 LHON
• Conservation: PhyloP100: -0.327
• Publications: 8 publications found

Genes affected

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]

TRNT (HGNC:7499): (mitochondrially encoded tRNA threonine)

TRNP (HGNC:7494): (mitochondrially encoded tRNA proline)

TRNP Gene-Disease associations (from GenCC):

• MERRF syndrome

  Inheritance: Mitochondrial Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, G2P
• mitochondrial disease

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Apogee2 supports a benign effect, 0.09807686 < 0.5 .
• BP6: Variant M-15812-G-A is Benign according to our data. Variant chrM-15812-G-A is described in ClinVar as Benign. ClinVar VariationId is 9675.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: High frequency in mitomap database: 0.0084
• BS2: High AC in GnomadMitoHomoplasmic at 656

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361789.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT-CYB	ENST00000361789.2	TSL:6	c.1066G>A	p.Val356Met	missense	Exon 1 of 1	ENSP00000354554.2
	MT-TT	ENST00000387460.2	TSL:6	n.-76G>A		upstream_gene	N/A
	MT-TP	ENST00000387461.2	TSL:6	n.*144C>T		downstream_gene	N/A

Frequencies

Mitomap GenBank AF: 0.0084 AC: 513

Gnomad homoplasmic AF: 0.012 AC: 656 AN: 56424

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56424

Alfa AF: 0.0152 Hom.: 203

Mitomap

Disease(s): LHON

Status: Reported-/-Secondary

ClinVar

Significance: Benign

Submissions summary: Pathogenic:1 Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Leber optic atrophy Pathogenic:1

Jan 01, 1992

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

Leigh syndrome Benign:1

Oct 17, 2019

Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The NC_012920.1:m.15812G>A (YP_003024038.1:p.Val356Met) variant in MTCYB gene is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BA1

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
Apogee2	Benign	0.098
Hmtvar	Benign	0.14
AlphaMissense	Benign	0.095
PhyloP100		-0.33
Mutation Taster		=75/25	polymorphism

Other links and lift over

dbSNP: rs200336777; hg19: chrM-15813;