Variant rs200715932 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP6_ModerateBP7BS2

The ENST00000361851.1(MT-ATP8):c.45C>T(p.Pro15=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Mitomap GenBank:

𝑓 0.0018 ( AC: 109 )

Consequence

MT-ATP8
ENST00000361851.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

No linked disesase in Mitomap

Conservation

PhyloP100: -7.49

Variant links:

Genes affected

ATP8 (HGNC:):

ATP8 links:

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-ATP8 links:

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

MT-TK links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP6

Variant M-8410-C-T is Benign according to our data. Variant chrM-8410-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 235707.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-7.49 with no splicing effect.

BS2

High AC in GnomadMitoHomoplasmic at 360

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP8	ATP8.1 use as main transcript	c.45C>T	p.Pro15=	synonymous_variant	1/1		YP_003024030.1
TRNK	TRNK.1 use as main transcript			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT-ATP8	ENST00000361851.1 linkuse as main transcript	c.45C>T	p.Pro15=	synonymous_variant	1/1			ENSP00000355265	P1
MT-TK	ENST00000387421.1 linkuse as main transcript			downstream_gene_variant

Frequencies

GnomAD4 exome

Cov.:

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

Mitomap GenBank

AF:

0.0018

AC:

109

Gnomad homoplasmic

AF:

0.0064

AC:

360

AN:

56427

Gnomad heteroplasmic

AF:

0.000089

AC:

AN:

56427

Alfa

AF:

0.00359

Hom.:

Mitomap

No disease associated.

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Mar 18, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.