1-155610453-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_018116.4(MSTO1):​c.113C>T​(p.Ser38Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S38C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 19)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MSTO1
NM_018116.4 missense

Scores

4
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.414
Variant links:
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 -2 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.10719156).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MSTO1NM_018116.4 linkc.113C>T p.Ser38Phe missense_variant Exon 2 of 14 ENST00000245564.8 NP_060586.2 Q9BUK6-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MSTO1ENST00000245564.8 linkc.113C>T p.Ser38Phe missense_variant Exon 2 of 14 1 NM_018116.4 ENSP00000245564.3 Q9BUK6-1
MSTO1ENST00000368341.8 linkc.113C>T p.Ser38Phe missense_variant Exon 2 of 13 2 ENSP00000357325.4 Q9BUK6-7

Frequencies

GnomAD3 genomes
Cov.:
19
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
698302
Hom.:
0
Cov.:
9
AF XY:
0.00
AC XY:
0
AN XY:
361112
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
19

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.20
T
BayesDel_noAF
Benign
-0.52
CADD
Benign
15
DANN
Benign
0.96
DEOGEN2
Benign
0.050
.;T;.
Eigen
Benign
-0.80
Eigen_PC
Benign
-0.99
FATHMM_MKL
Benign
0.033
N
LIST_S2
Benign
0.58
T;T;T
M_CAP
Benign
0.012
T
MetaRNN
Benign
0.11
T;T;T
MetaSVM
Benign
-0.93
T
MutationAssessor
Benign
1.1
.;L;L
PrimateAI
Uncertain
0.58
T
PROVEAN
Uncertain
-2.5
.;N;N
REVEL
Benign
0.094
Sift
Uncertain
0.019
.;D;D
Sift4G
Uncertain
0.050
.;T;T
Polyphen
0.58
.;P;.
Vest4
0.072, 0.089
MutPred
0.36
Loss of disorder (P = 0.0216);Loss of disorder (P = 0.0216);Loss of disorder (P = 0.0216);
MVP
0.42
MPC
2.2
ClinPred
0.25
T
GERP RS
-1.8
Varity_R
0.043
gMVP
0.31

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs1006121390; hg19: chr1-155580244; API