chr1-155609989-C-T

Variant names:

• chr1-155609989-C-T
• rs116421560
• XM_047424007.1:c.-260C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000697770.1(MSTO1):​c.-378-1050C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00657 in 501,810 control chromosomes in the GnomAD database, including 107 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.018 (90 hom., cov: 29)
  • Exomes 𝑓: 0.0017 (17 hom.)
• Consequence: MSTO1 ENST00000697770.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -3.11
• 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: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 1-155609989-C-T is Benign according to our data. Variant chr1-155609989-C-T is described in ClinVar as Benign. ClinVar VariationId is 1260671.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0603 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697770.1. 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.-260C>T		upstream_gene	N/A	NP_060586.2
	MSTO1	NM_001256532.1		c.-260C>T		upstream_gene	N/A	NP_001243461.1	Q9BUK6-2
	MSTO1	NM_001350772.1		c.-260C>T		upstream_gene	N/A	NP_001337701.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSTO1	ENST00000697770.1		c.-378-1050C>T		intron	N/A	ENSP00000513434.1	A0A8V8TLP0
	ENSG00000232519	ENST00000456382.2	TSL:5	n.104-97G>A		intron	N/A
	MSTO1	ENST00000245564.8	TSL:1 MANE Select	c.-260C>T		upstream_gene	N/A	ENSP00000245564.3	Q9BUK6-1

Frequencies

GnomAD3 genomes AF: 0.0176 AC: 2684 AN: 152188 Hom.: 89 Cov.: 29

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00373

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000206

Gnomad OTH AF: 0.0129

GnomAD4 exome AF: 0.00174 AC: 609 AN: 349504 Hom.: 17 AF XY: 0.00150 AC XY: 275 AN XY: 183220

African (AFR) AF: 0.0567 AC: 456 AN: 8048

American (AMR) AF: 0.00272 AC: 29 AN: 10658

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10740

East Asian (EAS) AF: 0.00 AC: 0 AN: 22998

South Asian (SAS) AF: 0.000265 AC: 9 AN: 34008

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24154

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1594

European-Non Finnish (NFE) AF: 0.000175 AC: 38 AN: 216530

Other (OTH) AF: 0.00371 AC: 77 AN: 20774

GnomAD4 genome AF: 0.0176 AC: 2687 AN: 152306 Hom.: 90 Cov.: 29 AF XY: 0.0172 AC XY: 1282 AN XY: 74484

African (AFR) AF: 0.0623 AC: 2587 AN: 41534

American (AMR) AF: 0.00372 AC: 57 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10632

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000206 AC: 14 AN: 68024

Other (OTH) AF: 0.0128 AC: 27 AN: 2116

Alfa AF: 0.00162 Hom.: 0

Bravo AF: 0.0196

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.30
DANN	Benign	0.79
PhyloP100		-3.1
PromoterAI		-0.014	Neutral

Splicing

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

Other links and lift over

dbSNP: rs116421560; hg19: chr1-155579780;