rs1556423442
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Mitomap GenBank:
𝑓 0.0051 ( AC: 311 )
Consequence
ATP8
missense
missense
Scores
Apogee2
Benign
Clinical Significance
Reversible-brain-pseudoatrophy
Conservation
PhyloP100: -0.220
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant M-8393-C-T is Benign according to our data. Variant chrM-8393-C-T is described in ClinVar as [Benign]. Clinvar id is 9638.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
High frequency in mitomap database: 0.0050999997
BS2
High AC in GnomadMitoHomoplasmic at 274
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP8 | unassigned_transcript_4805 use as main transcript | c.28C>T | p.Pro10Ser | missense_variant | 1/1 | |||
TRNK | unassigned_transcript_4804 use as main transcript | c.*29C>T | downstream_gene_variant | |||||
use as main transcript |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|
Frequencies
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
AC:
311
Gnomad homoplasmic
AF:
AC:
274
AN:
56434
Gnomad heteroplasmic
AF:
AC:
2
AN:
56434
Alfa
AF:
Hom.:
Mitomap
Reversible-brain-pseudoatrophy
ClinVar
Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Leigh syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Oct 17, 2019 | The NC_012920.1:m.8393C>T (YP_003024030.1:p.Pro10Ser) variant in MTATP8 gene is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BS1, BS2 - |
Brain pseudoatrophy, reversible, valproate-induced, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Nov 14, 2006 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Apogee2
Benign
Hmtvar
Pathogenic
AlphaMissense
Benign
BayesDel_addAF
Benign
T
DEOGEN2
Benign
T
LIST_S2
Benign
T
PROVEAN
Benign
N
Sift
Benign
T
Sift4G
Benign
T
GERP RS
Varity_R
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at