20-62201219-A-T

Variant names:

• chr20-62201219-A-T
• rs2184161
• NM_015666.4:c.*142A>T

Variant summary

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

The NM_015666.4(MTG2):​c.*142A>T variant causes a 3 prime UTR 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MTG2 NM_015666.4 3_prime_UTR
• 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: 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=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015666.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTG2	NM_015666.4	MANE Select	c.*142A>T		3_prime_UTR	Exon 7 of 7	NP_056481.1
	MTG2	NM_001384347.1		c.*142A>T		3_prime_UTR	Exon 7 of 7	NP_001371276.1
	MTG2	NM_001384348.1		c.827-1865A>T		intron	N/A	NP_001371277.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTG2	ENST00000370823.8	TSL:5 MANE Select	c.*142A>T		3_prime_UTR	Exon 7 of 7	ENSP00000359859.3
	MTG2	ENST00000467101.5	TSL:1	n.*827A>T		non_coding_transcript_exon	Exon 6 of 6	ENSP00000435214.1
	MTG2	ENST00000467101.5	TSL:1	n.*827A>T		3_prime_UTR	Exon 6 of 6	ENSP00000435214.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 905786 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 449842

African (AFR) AF: 0.00 AC: 0 AN: 20908

American (AMR) AF: 0.00 AC: 0 AN: 18812

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16486

East Asian (EAS) AF: 0.00 AC: 0 AN: 33060

South Asian (SAS) AF: 0.00 AC: 0 AN: 54812

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29822

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2896

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 687900

Other (OTH) AF: 0.00 AC: 0 AN: 41090

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.56
PhyloP100		0.31
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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;