rs8179271

chr1-155566947-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000697770.1(MSTO1):c.-379+3618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0594 in 152,030 control chromosomes in the GnomAD database, including 1,555 homozygotes. 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 0.059 (1555 hom., cov: 31)
• Consequence: MSTO1 ENST00000697770.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSTO1	XM_047424007.1	c.-608+3618G>A		intron_variant
MSTO1	XM_047424008.1	c.-524+3618G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSTO1	ENST00000697770.1	c.-379+3618G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0593 AC: 9010 AN: 151912 Hom.: 1549 Cov.: 31

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0135

Gnomad OTH AF: 0.0576

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

GnomAD4 genome AF: 0.0594 AC: 9023 AN: 152030 Hom.: 1555 Cov.: 31 AF XY: 0.0683 AC XY: 5076 AN XY: 74298

Gnomad4 AFR AF: 0.0133

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.0626

Gnomad4 NFE AF: 0.0135

Gnomad4 OTH AF: 0.0556

Alfa AF: 0.0327 Hom.: 182

Bravo AF: 0.0699

Asia WGS AF: 0.403 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.3
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8179271; hg19: chr1-155536738;