rs2184161

chr20-62201219-A-Gchr20-62201219-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MTG2	NM_015666.4	c.*142A>G		3_prime_UTR_variant	7/7	ENST00000370823.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTG2	ENST00000370823.8	c.*142A>G		3_prime_UTR_variant	7/7	5	NM_015666.4	P1
MTG2	ENST00000467101.5	c.*827A>G		3_prime_UTR_variant, NMD_transcript_variant	6/6	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

Gnomad4 AFR exome AF: 0.538

Gnomad4 AMR exome AF: 0.709

Gnomad4 ASJ exome AF: 0.542

Gnomad4 EAS exome AF: 0.903

Gnomad4 SAS exome AF: 0.777

Gnomad4 FIN exome AF: 0.592

Gnomad4 NFE exome AF: 0.519

Gnomad4 OTH exome AF: 0.564

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

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.565

Alfa AF: 0.534 Hom.: 19831

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

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

Other links and lift over

dbSNP: rs2184161; hg19: chr20-60776275;