dbSNP rs2184161: MTG2:c.*142A>G (chr20-62201219-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015666.4(MTG2):c.*142A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 1,056,052 control chromosomes in the GnomAD database, including 170,219 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 0.57 ( 24987 hom., cov: 33)

Exomes 𝑓: 0.56 ( 145232 hom. )

Consequence

MTG2
NM_015666.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.306

Publications

22 publications found

Variant links:

Genes affected

MTG2 (HGNC:16239): (mitochondrial ribosome associated GTPase 2) Small G proteins, such as GTPBP5, act as molecular switches that play crucial roles in the regulation of fundamental cellular processes such as protein synthesis, nuclear transport, membrane trafficking, and signal transduction (Hirano et al., 2006 [PubMed 17054726]).[supplied by OMIM, Mar 2008]

MTG2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015666.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MTG2	NM_015666.4	MANE Select	c.*142A>G	3_prime_UTR	Exon 7 of 7	NP_056481.1
MTG2	NM_001384347.1		c.*142A>G	3_prime_UTR	Exon 7 of 7	NP_001371276.1
MTG2	NM_001384348.1		c.827-1865A>G	intron	N/A	NP_001371277.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MTG2	ENST00000370823.8	TSL:5 MANE Select	c.*142A>G	3_prime_UTR	Exon 7 of 7	ENSP00000359859.3
MTG2	ENST00000467101.5	TSL:1	n.*827A>G	non_coding_transcript_exon	Exon 6 of 6	ENSP00000435214.1
MTG2	ENST00000467101.5	TSL:1	n.*827A>G	3_prime_UTR	Exon 6 of 6	ENSP00000435214.1

Frequencies

GnomAD3 genomes

AF:

0.566

AC:

86069

AN:

152020

Hom.:

24948

Cov.:

show subpopulations

Gnomad AFR

AF:

0.534

Gnomad AMI

AF:

0.426

Gnomad AMR

AF:

0.650

Gnomad ASJ

AF:

0.534

Gnomad EAS

AF:

0.888

Gnomad SAS

AF:

0.794

Gnomad FIN

AF:

0.597

Gnomad MID

AF:

0.548

Gnomad NFE

AF:

0.525

Gnomad OTH

AF:

0.560

GnomAD4 exome

AF:

0.558

AC:

504023

AN:

903914

Hom.:

145232

Cov.:

AF XY:

0.564

AC XY:

253409

AN XY:

448966

show subpopulations

African (AFR)

AF:

0.538

AC:

11221

AN:

20852

American (AMR)

AF:

0.709

AC:

13310

AN:

18784

Ashkenazi Jewish (ASJ)

AF:

0.542

AC:

8932

AN:

16468

East Asian (EAS)

AF:

0.903

AC:

29836

AN:

33054

South Asian (SAS)

AF:

0.777

AC:

42537

AN:

54772

European-Finnish (FIN)

AF:

0.592

AC:

17641

AN:

29804

Middle Eastern (MID)

AF:

0.540

AC:

1564

AN:

2896

European-Non Finnish (NFE)

AF:

0.519

AC:

355838

AN:

686262

Other (OTH)

AF:

0.564

AC:

23144

AN:

41022

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

10572

21144

31717

42289

52861

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9248

18496

27744

36992

46240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.566

AC:

86156

AN:

152138

Hom.:

24987

Cov.:

AF XY:

0.576

AC XY:

42857

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.534

AC:

22171

AN:

41504

American (AMR)

AF:

0.650

AC:

9942

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.534

AC:

1849

AN:

3464

East Asian (EAS)

AF:

0.887

AC:

4589

AN:

5172

South Asian (SAS)

AF:

0.795

AC:

3835

AN:

4826

European-Finnish (FIN)

AF:

0.597

AC:

6331

AN:

10602

Middle Eastern (MID)

AF:

0.551

AC:

161

AN:

292

European-Non Finnish (NFE)

AF:

0.525

AC:

35699

AN:

67970

Other (OTH)

AF:

0.565

AC:

1191

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1926

3853

5779

7706

9632

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

752

1504

2256

3008

3760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.543

Hom.:

30652

Bravo

AF:

0.564

Asia WGS

AF:

0.830

AC:

2883

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.5

(source)

DANN

Benign

0.36

PhyloP100

0.31

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over