Variant 6-73492090-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_012123.4(MTO1):c.1638-144C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 531,814 control chromosomes in the GnomAD database, including 118,648 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.63 ( 29620 hom., cov: 26)

Exomes 𝑓: 0.67 ( 89028 hom. )

Consequence

MTO1
NM_012123.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.205

Variant links:

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]

MTO1 links:

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]

EEF1A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BP6

Variant 6-73492090-C-T is Benign according to our data. Variant chr6-73492090-C-T is described in ClinVar as [Benign]. Clinvar id is 1291360.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
MTO1	NM_012123.4 linkuse as main transcript	c.1638-144C>T	intron_variant	ENST00000498286.6	NP_036255.2
MTO1	NM_001123226.2 linkuse as main transcript	c.1758-144C>T	intron_variant		NP_001116698.1
MTO1	NM_133645.3 linkuse as main transcript	c.1713-144C>T	intron_variant		NP_598400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTO1	ENST00000498286.6 linkuse as main transcript	c.1638-144C>T		intron_variant		1	NM_012123.4	ENSP00000419561	P1	Q9Y2Z2-4

Frequencies

GnomAD3 genomes

AF:

0.631

AC:

93006

AN:

147388

Hom.:

29624

Cov.:

show subpopulations

Gnomad AFR

AF:

0.481

Gnomad AMI

AF:

0.737

Gnomad AMR

AF:

0.617

Gnomad ASJ

AF:

0.653

Gnomad EAS

AF:

0.548

Gnomad SAS

AF:

0.725

Gnomad FIN

AF:

0.729

Gnomad MID

AF:

0.569

Gnomad NFE

AF:

0.704

Gnomad OTH

AF:

0.617

GnomAD4 exome

AF:

0.675

AC:

259310

AN:

384316

Hom.:

89028

Cov.:

AF XY:

0.677

AC XY:

139734

AN XY:

206390

show subpopulations

Gnomad4 AFR exome

AF:

0.445

Gnomad4 AMR exome

AF:

0.623

Gnomad4 ASJ exome

AF:

0.633

Gnomad4 EAS exome

AF:

0.508

Gnomad4 SAS exome

AF:

0.707

Gnomad4 FIN exome

AF:

0.707

Gnomad4 NFE exome

AF:

0.701

Gnomad4 OTH exome

AF:

0.655

GnomAD4 genome

AF:

0.631

AC:

93030

AN:

147498

Hom.:

29620

Cov.:

AF XY:

0.636

AC XY:

45598

AN XY:

71710

show subpopulations

Gnomad4 AFR

AF:

0.481

Gnomad4 AMR

AF:

0.617

Gnomad4 ASJ

AF:

0.653

Gnomad4 EAS

AF:

0.548

Gnomad4 SAS

AF:

0.725

Gnomad4 FIN

AF:

0.729

Gnomad4 NFE

AF:

0.704

Gnomad4 OTH

AF:

0.611

Alfa

AF:

0.647

Hom.:

3832

Bravo

AF:

0.602

Asia WGS

AF:

0.547

AC:

1901

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

3.6

DANN

Benign

0.48

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over