rs386829033

chrM-8392-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP7 BS1 BS2

The ENST00000361851.1(MT-ATP8):c.27G>A(p.Trp9=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Mitomap GenBank: 𝑓 0.0071 (AC: 431)
• Consequence: MT-ATP8 ENST00000361851.1 synonymous
• Clinical Significance: Not reported in ClinVar No linked disesase in Mitomap
• Conservation: PhyloP100: 2.89

Genes affected

ATP8 (HGNC:):

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-TK (HGNC:7489): (mitochondrially encoded tRNA lysine)

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP7: Synonymous conserved (PhyloP=2.89 with no splicing effect.
• BS1: High frequency in mitomap database: 0.0070999996
• BS2: High AC in GnomadMitoHomoplasmic at 63

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP8	ATP8.1	c.27G>A	p.Trp9=	synonymous_variant	1/1
TRNK	TRNK.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-ATP8	ENST00000361851.1	c.27G>A	p.Trp9=	synonymous_variant	1/1			P1
MT-TK	ENST00000387421.1			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: 0.0071 AC: 431

Gnomad homoplasmic AF: 0.0011 AC: 63 AN: 56406

Gnomad heteroplasmic AF: 0.0 AC: 0 AN: 56406

Alfa AF: 0.000445 Hom.: 2

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.42	T
MutationTaster	Benign	1.0	D
GERP RS		2.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs121434446; hg19: chrM-8393;