1-155610459-A-T

Variant names:

• chr1-155610459-A-T
• NM_018116.4:c.119A>T

Variant summary

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

The NM_018116.4(MSTO1):​c.119A>T​(p.Glu40Val) 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: not found (cov: 19)
• Consequence: MSTO1 NM_018116.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.09

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]

LOC105371452 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.095719725).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSTO1	NM_018116.4	c.119A>T	p.Glu40Val	missense_variant	Exon 2 of 14	ENST00000245564.8	NP_060586.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSTO1	ENST00000245564.8	c.119A>T	p.Glu40Val	missense_variant	Exon 2 of 14	1	NM_018116.4	ENSP00000245564.3
MSTO1	ENST00000368341.8	c.119A>T	p.Glu40Val	missense_variant	Exon 2 of 13	2		ENSP00000357325.4

Frequencies

GnomAD3 genomes Cov.: 19

GnomAD4 exome Cov.: 9

GnomAD4 genome Cov.: 19

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Dec 26, 2023

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.091
BayesDel_addAF	Benign	-0.083	T
BayesDel_noAF	Benign	-0.36
CADD	Benign	15
DANN	Benign	0.97
DEOGEN2	Benign	0.0055	.;T;.
Eigen	Benign	-0.77
Eigen_PC	Benign	-0.87
FATHMM_MKL	Benign	0.024	N
LIST_S2	Benign	0.65	T;T;T
M_CAP	Benign	0.0076	T
MetaRNN	Benign	0.096	T;T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	1.8	.;L;L
PrimateAI	Uncertain	0.64	T
PROVEAN	Benign	-1.4	.;N;N
REVEL	Benign	0.056
Sift	Benign	0.48	.;T;T
Sift4G	Benign	0.28	.;T;T
Polyphen		0.14	.;B;.
Vest4		0.16, 0.17
MutPred		0.44		Loss of disorder (P = 0.0272);Loss of disorder (P = 0.0272);Loss of disorder (P = 0.0272);
MVP		0.36
MPC		2.3
ClinPred		0.12	T
GERP RS		2.0
Varity_R		0.048
gMVP		0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-155580250;