1-155610045-CA-C

Variant names:

• chr1-155610045-CA-C
• rs1426035342
• XM_047424007.1:c.-203delA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000697770.1(MSTO1):​c.-378-993delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 152,108 control chromosomes in the GnomAD database, including 101 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.020 (101 hom., cov: 28)
• Consequence: MSTO1 ENST00000697770.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.32
• 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 -10 ACMG points.

• BP6: Variant 1-155610045-CA-C is Benign according to our data. Variant chr1-155610045-CA-C is described in ClinVar as Benign. ClinVar VariationId is 1270238.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0689 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.-203delA		upstream_gene	N/A	NP_060586.2
	MSTO1	NM_001256532.1		c.-203delA		upstream_gene	N/A	NP_001243461.1	Q9BUK6-2
	MSTO1	NM_001350772.1		c.-203delA		upstream_gene	N/A	NP_001337701.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSTO1	ENST00000697770.1		c.-378-993delA		intron	N/A	ENSP00000513434.1	A0A8V8TLP0
	ENSG00000232519	ENST00000456382.2	TSL:5	n.104-154delT		intron	N/A
	MSTO1	ENST00000245564.8	TSL:1 MANE Select	c.-203delA		upstream_gene	N/A	ENSP00000245564.3	Q9BUK6-1

Frequencies

GnomAD3 genomes AF: 0.0203 AC: 3081 AN: 151994 Hom.: 101 Cov.: 28

Gnomad AFR AF: 0.0712

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00543

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.000832

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000294

Gnomad OTH AF: 0.0148

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0203 AC: 3082 AN: 152108 Hom.: 101 Cov.: 28 AF XY: 0.0189 AC XY: 1404 AN XY: 74358

African (AFR) AF: 0.0710 AC: 2941 AN: 41420

American (AMR) AF: 0.00542 AC: 83 AN: 15306

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

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.000625 AC: 3 AN: 4802

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000294 AC: 20 AN: 67992

Other (OTH) AF: 0.0147 AC: 31 AN: 2112

Alfa AF: 0.0183 Hom.: 7

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1426035342; hg19: chr1-155579836;