rs2151511

Variant names:

• chr20-62201388-A-G
• rs2151511
• ENST00000467101.5:n.*996A>G

Your query was ambiguous. Multiple possible variants found:

• chr20-62201388-A-G
• chr20-62201388-A-T

Variant summary

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

The ENST00000467101.5(MTG2):​n.*996A>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 0.582 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 ENST00000467101.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 12 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=-0.89).
• 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 rank	MANE	Protein	UniProt
MTG2	NM_015666.4	c.*311A>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.*996A>G		non_coding_transcript_exon_variant	Exon 6 of 6	1		ENSP00000435214.1
MTG2	ENST00000370823.8	c.*311A>G		3_prime_UTR_variant	Exon 7 of 7	5	NM_015666.4	ENSP00000359859.3
MTG2	ENST00000467101.5	n.*996A>G		3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000435214.1

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

African (AFR) AF: 0.543 AC: 3809 AN: 7014

American (AMR) AF: 0.702 AC: 5233 AN: 7456

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 3848 AN: 7096

East Asian (EAS) AF: 0.908 AC: 13128 AN: 14464

South Asian (SAS) AF: 0.779 AC: 17883 AN: 22958

European-Finnish (FIN) AF: 0.593 AC: 8311 AN: 14008

Middle Eastern (MID) AF: 0.538 AC: 554 AN: 1030

European-Non Finnish (NFE) AF: 0.530 AC: 72553 AN: 136976

Other (OTH) AF: 0.559 AC: 7368 AN: 13190

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

African (AFR) AF: 0.537 AC: 22310 AN: 41518

American (AMR) AF: 0.653 AC: 9979 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1857 AN: 3470

East Asian (EAS) AF: 0.884 AC: 4570 AN: 5172

South Asian (SAS) AF: 0.794 AC: 3834 AN: 4828

European-Finnish (FIN) AF: 0.597 AC: 6335 AN: 10608

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35740 AN: 67998

Other (OTH) AF: 0.564 AC: 1193 AN: 2116

Alfa AF: 0.552 Hom.: 3477

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
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2151511; hg19: chr20-60776444;