M-8529-G-A

Position:

• chrM-8529-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Mitomap GenBank: Absent
• Consequence: ATP6 start_lost
• Clinical Significance: Pathogenic no assertion criteria provided P:1 Apical-HCM
• Conservation: PhyloP100: 7.76

Genes affected

ATP6 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: No frequency data in Mitomap. Probably very rare.
• PP5: Variant M-8529-G-A is Pathogenic according to our data. Variant chrM-8529-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 9639.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP6	unassigned_transcript_4806	c.3G>A	p.Met1?	start_lost	1/1
ATP8	unassigned_transcript_4805	c.164G>A	p.Ter55Ter	stop_retained_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD4 exome Cov.: 0

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

Mitomap

Apical-HCM

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Cardiomyopathy, apical hypertrophic, and neuropathy Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 01, 2008

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.59	D
DEOGEN2	Benign	0.22	T
LIST_S2	Uncertain	0.90	D
PROVEAN	Uncertain	-3.3	D
GERP RS		5.1
Varity_R		0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs267606881; hg19: chrM-8530;