Variant chr10-133402163-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_138384.4(MTG1):c.588C>T(p.Pro196=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00708 in 1,614,036 control chromosomes in the GnomAD database, including 97 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0061 ( 7 hom., cov: 33)

Exomes 𝑓: 0.0072 ( 90 hom. )

Consequence

MTG1
NM_138384.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.125

Variant links:

Genes affected

MTG1 (HGNC:32159): (mitochondrial ribosome associated GTPase 1) Enables GTPase activity. Involved in regulation of mitochondrial translation and regulation of respiratory system process. Located in mitochondrial inner membrane and mitochondrial ribosome. [provided by Alliance of Genome Resources, Apr 2022]

MTG1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 10-133402163-C-T is Benign according to our data. Variant chr10-133402163-C-T is described in ClinVar as [Benign]. Clinvar id is 781793.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.125 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.00719 (10509/1461818) while in subpopulation SAS AF= 0.0163 (1406/86258). AF 95% confidence interval is 0.0156. There are 90 homozygotes in gnomad4_exome. There are 5560 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTG1	NM_138384.4 linkuse as main transcript	c.588C>T	p.Pro196=	synonymous_variant	8/11	ENST00000317502.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTG1	ENST00000317502.11 linkuse as main transcript	c.588C>T	p.Pro196=	synonymous_variant	8/11	1	NM_138384.4	P1	Q9BT17-1

Frequencies

GnomAD3 genomes

AF:

0.00609

AC:

926

AN:

152100

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00111

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.00773

Gnomad ASJ

AF:

0.0317

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0172

Gnomad FIN

AF:

0.000755

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00776

Gnomad OTH

AF:

0.00670

GnomAD3 exomes

AF:

0.00798

AC:

2007

AN:

251390

Hom.:

AF XY:

0.00898

AC XY:

1220

AN XY:

135896

show subpopulations

Gnomad AFR exome

AF:

0.00160

Gnomad AMR exome

AF:

0.00665

Gnomad ASJ exome

AF:

0.0330

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0151

Gnomad FIN exome

AF:

0.000601

Gnomad NFE exome

AF:

0.00765

Gnomad OTH exome

AF:

0.0116

GnomAD4 exome

AF:

0.00719

AC:

10509

AN:

1461818

Hom.:

Cov.:

AF XY:

0.00765

AC XY:

5560

AN XY:

727220

show subpopulations

Gnomad4 AFR exome

AF:

0.00146

Gnomad4 AMR exome

AF:

0.00691

Gnomad4 ASJ exome

AF:

0.0328

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0163

Gnomad4 FIN exome

AF:

0.000543

Gnomad4 NFE exome

AF:

0.00649

Gnomad4 OTH exome

AF:

0.00899

GnomAD4 genome

AF:

0.00606

AC:

922

AN:

152218

Hom.:

Cov.:

AF XY:

0.00602

AC XY:

448

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.00111

Gnomad4 AMR

AF:

0.00765

Gnomad4 ASJ

AF:

0.0317

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.0172

Gnomad4 FIN

AF:

0.000755

Gnomad4 NFE

AF:

0.00775

Gnomad4 OTH

AF:

0.00616

Alfa

AF:

0.00946

Hom.:

Bravo

AF:

0.00609

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.0111

EpiControl

AF:

0.0120

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

0.093

DANN

Benign

0.80

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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