1-155610299-C-T

Variant names:

• chr1-155610299-C-T
• rs757329280
• NM_018116.4:c.51C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001350776.1(MSTO1):​c.-237C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000545 in 1,101,166 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000067 (0 hom., cov: 27)
  • Exomes 𝑓: 0.0000052 (0 hom.)
• Consequence: MSTO1 NM_001350776.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• Publications: 0 publications found

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]

MSTO1 Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Broad Center for Mendelian Genomics, Ambry Genetics

ENSG00000232519 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350776.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSTO1	NM_018116.4	MANE Select	c.51C>T	p.Ala17Ala	synonymous	Exon 1 of 14	NP_060586.2
	MSTO1	NM_001350776.1		c.-237C>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 14	NP_001337705.1
	MSTO1	NM_001350777.1		c.-506C>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 14	NP_001337706.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSTO1	ENST00000245564.8	TSL:1 MANE Select	c.51C>T	p.Ala17Ala	synonymous	Exon 1 of 14	ENSP00000245564.3	Q9BUK6-1
	MSTO1	ENST00000368341.8	TSL:2	c.51C>T	p.Ala17Ala	synonymous	Exon 1 of 13	ENSP00000357325.4	Q9BUK6-7
	MSTO1	ENST00000490743.5	TSL:1	n.51C>T		non_coding_transcript_exon	Exon 1 of 13	ENSP00000476353.1	Q9BUK6-4

Frequencies

GnomAD3 genomes AF: 0.00000675 AC: 1 AN: 148216 Hom.: 0 Cov.: 27

Gnomad AFR AF: 0.0000251

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000525 AC: 5 AN: 952950 Hom.: 0 Cov.: 12 AF XY: 0.00000419 AC XY: 2 AN XY: 476920

African (AFR) AF: 0.00 AC: 0 AN: 22082

American (AMR) AF: 0.00 AC: 0 AN: 25758

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16994

East Asian (EAS) AF: 0.0000278 AC: 1 AN: 35924

South Asian (SAS) AF: 0.00 AC: 0 AN: 60416

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35306

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2886

European-Non Finnish (NFE) AF: 0.00000562 AC: 4 AN: 711112

Other (OTH) AF: 0.00 AC: 0 AN: 42472

GnomAD4 genome AF: 0.00000675 AC: 1 AN: 148216 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 AN XY: 72130

African (AFR) AF: 0.0000251 AC: 1 AN: 39906

American (AMR) AF: 0.00 AC: 0 AN: 14850

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3412

East Asian (EAS) AF: 0.00 AC: 0 AN: 5046

South Asian (SAS) AF: 0.00 AC: 0 AN: 4458

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10296

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 308

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67040

Other (OTH) AF: 0.00 AC: 0 AN: 2006

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	9.7
DANN	Benign	0.97
PhyloP100		-0.58
PromoterAI		-0.0074	Neutral
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs757329280; hg19: chr1-155580090;