chr1-155610453-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_018116.4(MSTO1):c.113C>G(p.Ser38Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000022 ( 0 hom., cov: 19)
Exomes 𝑓: 0.000011 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MSTO1
NM_018116.4 missense
NM_018116.4 missense
Scores
1
12
Clinical Significance
Conservation
PhyloP100: 0.414
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.104735166).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSTO1 | NM_018116.4 | c.113C>G | p.Ser38Cys | missense_variant | 2/14 | ENST00000245564.8 | |
LOC105371452 | XR_922171.2 | n.77-561G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSTO1 | ENST00000245564.8 | c.113C>G | p.Ser38Cys | missense_variant | 2/14 | 1 | NM_018116.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 3AN: 134080Hom.: 0 Cov.: 19 FAILED QC
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GnomAD3 exomes AF: 0.0000121 AC: 1AN: 82920Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 42974
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GnomAD4 exome AF: 0.0000115 AC: 8AN: 698300Hom.: 0 Cov.: 9 AF XY: 0.0000194 AC XY: 7AN XY: 361110
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000224 AC: 3AN: 134080Hom.: 0 Cov.: 19 AF XY: 0.0000156 AC XY: 1AN XY: 64154
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.113C>G (p.S38C) alteration is located in exon 2 (coding exon 2) of the MSTO1 gene. This alteration results from a C to G substitution at nucleotide position 113, causing the serine (S) at amino acid position 38 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
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
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N
PrimateAI
Uncertain
T
Polyphen
0.58
.;P;.
Vest4
0.10, 0.11
MutPred
Loss of disorder (P = 0.0125);Loss of disorder (P = 0.0125);Loss of disorder (P = 0.0125);
MVP
0.42
MPC
2.3
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