rs878853091

Variant names:

• chrM-8519-G-A
• rs878853091
• ENST00000361851.1:c.154G>A

Your query was ambiguous. Multiple possible variants found:

• chrM-8519-G-A
• chrM-8519-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4 BP6_Very_Strong BS2

The ENST00000361851.1(MT-ATP8):​c.154G>A​(p.Glu52Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E52G) has been classified as Likely benign.

• Frequency: Mitomap GenBank: 𝑓 0.0026 (AC: 159)
• Consequence: MT-ATP8 ENST00000361851.1 missense
• Scores: Apogee2 Benign 0.16
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3 Possible-susceptibility-to-bullous-pemphigoid
• Conservation: PhyloP100: -0.0270
• Publications: 10 publications found

Genes affected

MT-ATP8 (HGNC:7415): (mitochondrially encoded ATP synthase 8) Contributes to proton-transporting ATP synthase activity, rotational mechanism. Involved in mitochondrial ATP synthesis coupled proton transport. Part of mitochondrial proton-transporting ATP synthase complex. Implicated in multiple sclerosis and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]

MT-ATP6 (HGNC:7414): (mitochondrially encoded ATP synthase 6) Contributes to proton-transporting ATP synthase activity, rotational mechanism. Involved in mitochondrial ATP synthesis coupled proton transport. Part of mitochondrial proton-transporting ATP synthase complex. Implicated in Leber hereditary optic neuropathy; NARP syndrome; Parkinson's disease; multiple sclerosis; and systemic lupus erythematosus. [provided by Alliance of Genome Resources, Apr 2022]

MT-CO2 (HGNC:7421): (mitochondrially encoded cytochrome c oxidase II) Contributes to cytochrome-c oxidase activity. Predicted to be involved in mitochondrial electron transport, cytochrome c to oxygen and positive regulation of vasoconstriction. Located in mitochondrial inner membrane. Part of respiratory chain complex IV. Biomarker of Huntington's disease and stomach cancer. [provided by Alliance of Genome Resources, Apr 2022]

TRNK (HGNC:7489): (mitochondrially encoded tRNA lysine)

TRNK Gene-Disease associations (from GenCC):

• Leigh syndrome

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen
• mitochondrial disease

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen
• maternally-inherited cardiomyopathy and hearing loss

  Inheritance: Mitochondrial Classification: SUPPORTIVE Submitted by: Orphanet
• MERRF syndrome

  Inheritance: Mitochondrial Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Apogee2 supports a benign effect, 0.15815336 < 0.5 .
• BP6: Variant M-8519-G-A is Benign according to our data. Variant chrM-8519-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 235671.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High AC in GnomadMitoHomoplasmic at 144

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361851.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT-ATP8	ENST00000361851.1	TSL:6	c.154G>A	p.Glu52Lys	missense	Exon 1 of 1	ENSP00000355265.1	P03928
	MT-ATP6	ENST00000361899.2	TSL:6	c.-8G>A		upstream_gene	N/A	ENSP00000354632.2	P00846
	MT-CO2	ENST00000361739.1	TSL:6	c.*250G>A		downstream_gene	N/A	ENSP00000354876.1	P00403

Frequencies

Mitomap GenBank AF: 0.0026 AC: 159

Gnomad homoplasmic AF: 0.0026 AC: 144 AN: 56419

Gnomad heteroplasmic AF: 0.00012 AC: 7 AN: 56419

Alfa AF: 0.00378 Hom.: 17

Mitomap

Disease(s): Possible-susceptibility-to-bullous-pemphigoid

Status: Reported

ClinVar

ClinVar submissions

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)
-	-	1	Leigh syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
Apogee2	Benign	0.16
Hmtvar	Pathogenic	0.80
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.36	T
DEOGEN2	Benign	0.12	T
LIST_S2	Benign	0.79	T
PhyloP100		-0.027
PROVEAN	Uncertain	-3.1	D
Sift	Uncertain	0.028	D
Sift4G	Benign	0.068	T
GERP RS		1.8
Varity_R		0.29

Other links and lift over

dbSNP: rs878853091; hg19: chrM-8520;