rs2151511

chr20-62201388-A-Gchr20-62201388-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.*311A>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 0.582 in 376,398 control chromosomes in the GnomAD database, including 66,444 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 (25084 hom., cov: 34)
  • Exomes 𝑓: 0.59 (41360 hom.)
• Consequence: MTG2 NM_015666.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTG2	NM_015666.4	c.*311A>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.*311A>G		3_prime_UTR_variant	7/7	5	NM_015666.4	P1
MTG2	ENST00000467101.5	c.*996A>G		3_prime_UTR_variant, NMD_transcript_variant	6/6	1

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86282 AN: 152088 Hom.: 25045 Cov.: 34

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.559

GnomAD4 exome AF: 0.592 AC: 132687 AN: 224192 Hom.: 41360 Cov.: 2 AF XY: 0.602 AC XY: 70771 AN XY: 117510

Gnomad4 AFR exome AF: 0.543

Gnomad4 AMR exome AF: 0.702

Gnomad4 ASJ exome AF: 0.542

Gnomad4 EAS exome AF: 0.908

Gnomad4 SAS exome AF: 0.779

Gnomad4 FIN exome AF: 0.593

Gnomad4 NFE exome AF: 0.530

Gnomad4 OTH exome AF: 0.559

GnomAD4 genome AF: 0.567 AC: 86369 AN: 152206 Hom.: 25084 Cov.: 34 AF XY: 0.578 AC XY: 42980 AN XY: 74420

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.564

Alfa AF: 0.553 Hom.: 3370

Bravo AF: 0.566

Asia WGS AF: 0.829 AC: 2882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.042
Dann	Benign	0.13

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2151511; hg19: chr20-60776444;