6-73491003-A-G

Variant names:

• chr6-73491003-A-G
• rs577372
• NM_012123.4:c.1638-1231A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012123.4(MTO1):​c.1638-1231A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,958 control chromosomes in the GnomAD database, including 26,828 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 0.58 (26828 hom., cov: 32)
• Consequence: MTO1 NM_012123.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.951
• Publications: 10 publications found

Genes affected

MTO1 (HGNC:19261): (mitochondrial tRNA translation optimization 1) This gene encodes a mitochondrial protein thought to be involved in mitochondrial tRNA modification. The encoded protein may also play a role in the expression of the non-syndromic and aminoglycoside-induced deafness phenotypes associated with a specific mutation in the mitochondrial 12S rRNA gene. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

EEF1A1 (HGNC:3189): (eukaryotic translation elongation factor 1 alpha 1) This gene encodes an isoform of the alpha subunit of the elongation factor-1 complex, which is responsible for the enzymatic delivery of aminoacyl tRNAs to the ribosome. This isoform (alpha 1) is expressed in brain, placenta, lung, liver, kidney, and pancreas, and the other isoform (alpha 2) is expressed in brain, heart and skeletal muscle. This isoform is identified as an autoantigen in 66% of patients with Felty syndrome. This gene has been found to have multiple copies on many chromosomes, some of which, if not all, represent different pseudogenes. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTO1	NM_012123.4	c.1638-1231A>G		intron_variant	Intron 9 of 11	ENST00000498286.6	NP_036255.2
MTO1	NM_001123226.2	c.1758-1231A>G		intron_variant	Intron 10 of 12		NP_001116698.1
MTO1	NM_133645.3	c.1713-1231A>G		intron_variant	Intron 10 of 12		NP_598400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTO1	ENST00000498286.6	c.1638-1231A>G		intron_variant	Intron 9 of 11	1	NM_012123.4	ENSP00000419561.2

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88181 AN: 151838 Hom.: 26841 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.580 AC: 88162 AN: 151958 Hom.: 26828 Cov.: 32 AF XY: 0.581 AC XY: 43145 AN XY: 74264

African (AFR) AF: 0.421 AC: 17462 AN: 41450

American (AMR) AF: 0.448 AC: 6834 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2216 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2360 AN: 5152

South Asian (SAS) AF: 0.679 AC: 3276 AN: 4822

European-Finnish (FIN) AF: 0.684 AC: 7227 AN: 10564

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.688 AC: 46752 AN: 67944

Other (OTH) AF: 0.571 AC: 1206 AN: 2112

Alfa AF: 0.634 Hom.: 93649

Bravo AF: 0.554

Asia WGS AF: 0.488 AC: 1700 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	0.14
DANN	Benign	0.71
PhyloP100		-0.95
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs577372; hg19: chr6-74200726;