chr20-62201219-A-G

Variant names:

• chr20-62201219-A-G
• rs2184161
• ENST00000467101.5:n.*827A>G

Variant summary

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

The ENST00000467101.5(MTG2):​n.*827A>G variant causes a non coding transcript exon 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 ENST00000467101.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 22 publications found

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]

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTG2	NM_015666.4	c.*142A>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000370823.8	NP_056481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTG2	ENST00000467101.5	n.*827A>G		non_coding_transcript_exon_variant	Exon 6 of 6	1		ENSP00000435214.1
MTG2	ENST00000370823.8	c.*142A>G		3_prime_UTR_variant	Exon 7 of 7	5	NM_015666.4	ENSP00000359859.3
MTG2	ENST00000467101.5	n.*827A>G		3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000435214.1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86069 AN: 152020 Hom.: 24948 Cov.: 33

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.: 12 AF XY: 0.564 AC XY: 253409 AN XY: 448966

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

GnomAD4 genome AF: 0.566 AC: 86156 AN: 152138 Hom.: 24987 Cov.: 33 AF XY: 0.576 AC XY: 42857 AN XY: 74370

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

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.36
PhyloP100		0.31
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: rs2184161; hg19: chr20-60776275;