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

Scores

Apogee2
Benign
0.048

Clinical Significance

Benign criteria provided, single submitter B:1O:1
Reversible-brain-pseudoatrophy

Conservation

PhyloP100: -0.220
Variant links:
Genes affected

Genome browser will be placed here

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
ATP8unassigned_transcript_4805 use as main transcriptc.28C>T p.Pro10Ser missense_variant 1/1
TRNKunassigned_transcript_4804 use as main transcriptc.*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
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.0051
AC:
311
Gnomad homoplasmic
AF:
0.0049
AC:
274
AN:
56434
Gnomad heteroplasmic
AF:
0.000035
AC:
2
AN:
56434
Alfa
AF:
0.00779
Hom.:
35

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 submitterclinical testingWong Mito Lab, Molecular and Human Genetics, Baylor College of MedicineOct 17, 2019The 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variant in MTATP8 gene is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished).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 providedliterature onlyOMIMNov 14, 2006- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Apogee2
Benign
0.048
Hmtvar
Pathogenic
0.67
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.42
T
DEOGEN2
Benign
0.041
T
LIST_S2
Benign
0.65
T
PROVEAN
Benign
-1.3
N
Sift
Benign
0.21
T
Sift4G
Benign
0.23
T
GERP RS
-2.9
Varity_R
0.066

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.

Other links and lift over

dbSNP: rs1556423442; hg19: chrM-8394; API