1-155611098-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_018116.4(MSTO1):c.280G>A(p.Ala94Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0016 ( 0 hom., cov: 15)
Exomes 𝑓: 0.00019 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MSTO1
NM_018116.4 missense
NM_018116.4 missense
Scores
12
Clinical Significance
Conservation
PhyloP100: 1.07
Genes affected
MSTO1 (HGNC:29678): (misato mitochondrial distribution and morphology regulator 1) Involved in mitochondrion distribution. Located in cytosol and mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.004330635).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSTO1 | NM_018116.4 | c.280G>A | p.Ala94Thr | missense_variant | 3/14 | ENST00000245564.8 | |
LOC105371452 | XR_922171.2 | n.77-1206C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSTO1 | ENST00000245564.8 | c.280G>A | p.Ala94Thr | missense_variant | 3/14 | 1 | NM_018116.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 187AN: 120530Hom.: 0 Cov.: 15 FAILED QC
GnomAD3 genomes
?
AF:
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187
AN:
120530
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15
FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000187 AC: 150AN: 801542Hom.: 0 Cov.: 11 AF XY: 0.000137 AC XY: 56AN XY: 408512
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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11
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00158 AC: 191AN: 120630Hom.: 0 Cov.: 15 AF XY: 0.00162 AC XY: 92AN XY: 56616
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?
Data not reliable, filtered out with message: AS_VQSR
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ExAC
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27
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Mar 26, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
Polyphen
0.0030
.;B;.
Vest4
0.095, 0.15
MVP
0.15
MPC
1.8
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at