rs1556424448

Positions:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Mitomap GenBank:
𝑓 0.0 ( AC: 2 )

Consequence

ND6
missense

Scores

Apogee2
Pathogenic
0.76

Clinical Significance

Uncertain significance criteria provided, single submitter U:1
No linked disesase in Mitomap

Conservation

PhyloP100: 5.72
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very low frequency in mitomap database: 0.0

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ND6unassigned_transcript_4817 use as main transcriptc.197T>C p.Val66Ala missense_variant 1/1
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:
0.0
AC:
2
Gnomad homoplasmic
AF:
0.0
AC:
0
AN:
56434
Gnomad heteroplasmic
AF:
0.000018
AC:
1
AN:
56434

Mitomap

No disease associated.

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Headache;C0030554:Paresthesia;C0037763:Muscle spasm;C0042571:Vertigo;C0235095:Constriction of peripheral visual field;C0338656:Cognitive impairment;C4021085:Abnormal brain morphology Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingCentre for Mendelian Genomics, University Medical Centre LjubljanaJan 01, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Apogee2
Pathogenic
0.76
Hmtvar
Pathogenic
0.80
AlphaMissense
Pathogenic
0.90
BayesDel_addAF
Benign
-0.027
T
DEOGEN2
Pathogenic
0.85
D
LIST_S2
Benign
0.74
T
MutationAssessor
Pathogenic
3.5
H
PROVEAN
Uncertain
-4.0
D
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
GERP RS
4.0
Varity_R
0.84

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: rs1556424448; hg19: chrM-14478; API