rs28359178

Variant names:

• chrM-13708-G-A
• rs28359178
• ENST00000361567.2:c.1372G>A

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4 BP6_Very_Strong BA1

The ENST00000361567.2(MT-ND5):​c.1372G>A​(p.Ala458Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency: Mitomap GenBank: 𝑓 0.075 (AC: 4560)
• Consequence: MT-ND5 ENST00000361567.2 missense
• Scores: Apogee2 Benign 0.31
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts P:1 U:1 B:2 LHON-/-Increased-MS-risk-/-higher-freq-in-PD-ADS
• Conservation: PhyloP100: 0.633
• Publications: 95 publications found

Genes affected

MT-ND5 (HGNC:7461): (mitochondrially encoded NADH dehydrogenase 5) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; Leigh disease; and MELAS syndrome. [provided by Alliance of Genome Resources, Apr 2022]

MT-ND5 Gene-Disease associations (from GenCC):

• Leigh syndrome

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

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen
• Leber hereditary optic neuropathy

  Inheritance: Mitochondrial Classification: STRONG, SUPPORTIVE Submitted by: G2P, Orphanet
• maternally-inherited Leigh syndrome

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

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

  Inheritance: Mitochondrial Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -17 ACMG points.

• BP4: Apogee2 supports a benign effect, 0.30702576 < 0.5 .
• BP6: Variant M-13708-G-A is Benign according to our data. Variant chrM-13708-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 9696.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: High frequency in mitomap database: 0.0746

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361567.2. 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-ND5	ENST00000361567.2	TSL:6	c.1372G>A	p.Ala458Thr	missense	Exon 1 of 1	ENSP00000354813.2	P03915

Frequencies

Mitomap GenBank AF: 0.075 AC: 4560

Gnomad homoplasmic AF: 0.076 AC: 4263 AN: 56361

Gnomad heteroplasmic AF: 0.00037 AC: 21 AN: 56361

Alfa AF: 0.114 Hom.: 2906

Mitomap

Disease(s): LHON-/-Increased-MS-risk-/-higher-freq-in-PD-ADS

Status: Conflicting-reports

ClinVar

ClinVar submissions

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
1	1	-	Leber optic atrophy (2)
-	-	1	Leigh syndrome (1)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
Apogee2	Benign	0.31
Hmtvar	Benign	0.21
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.41	T
DEOGEN2	Benign	0.030	T
LIST_S2	Benign	0.58	T
MutationAssessor	Benign	1.6	L
PhyloP100		0.63
PROVEAN	Benign	-1.5	N
Sift4G	Benign	0.078	T
GERP RS		-5.7
Varity_R		0.29
Mutation Taster		=95/5	polymorphism

Other links and lift over

dbSNP: rs28359178; hg19: chrM-13709;