20-62201388-A-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000467101.5(MTG2):​n.*996A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000467101.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTG2	NM_015666.4	MANE Select	c.*311A>T		3_prime_UTR	Exon 7 of 7	NP_056481.1
	MTG2	NR_169197.1		n.1567A>T		non_coding_transcript_exon	Exon 7 of 8
	MTG2	NR_169198.1		n.1567A>T		non_coding_transcript_exon	Exon 7 of 8

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTG2	ENST00000467101.5	TSL:1	n.*996A>T		non_coding_transcript_exon	Exon 6 of 6	ENSP00000435214.1
	MTG2	ENST00000370823.8	TSL:5 MANE Select	c.*311A>T		3_prime_UTR	Exon 7 of 7	ENSP00000359859.3
	MTG2	ENST00000467101.5	TSL:1	n.*996A>T		3_prime_UTR	Exon 6 of 6	ENSP00000435214.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 224930 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 117898

African (AFR) AF: 0.00 AC: 0 AN: 7032

American (AMR) AF: 0.00 AC: 0 AN: 7480

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7108

East Asian (EAS) AF: 0.00 AC: 0 AN: 14476

South Asian (SAS) AF: 0.00 AC: 0 AN: 22992

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 14054

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1038

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 137508

Other (OTH) AF: 0.00 AC: 0 AN: 13242

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.036
DANN	Benign	0.24
PhyloP100		-1.0

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;