rs2265638

Positions:

• chr10-133403671-C-T

Variant summary

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

The NM_138384.4(MTG1):​c.752+898C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,132 control chromosomes in the GnomAD database, including 24,052 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 0.53 (24052 hom., cov: 32)
• Consequence: MTG1 NM_138384.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97

Genes affected

MTG1 (HGNC:32159): (mitochondrial ribosome associated GTPase 1) Enables GTPase activity. Involved in regulation of mitochondrial translation and regulation of respiratory system process. Located in mitochondrial inner membrane and mitochondrial ribosome. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTG1	NM_138384.4	c.752+898C>T		intron_variant		ENST00000317502.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTG1	ENST00000317502.11	c.752+898C>T		intron_variant		1	NM_138384.4	P1

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80907 AN: 152014 Hom.: 24034 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.550

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.532 AC: 80945 AN: 152132 Hom.: 24052 Cov.: 32 AF XY: 0.534 AC XY: 39689 AN XY: 74364

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.556

Alfa AF: 0.637 Hom.: 51501

Bravo AF: 0.506

Asia WGS AF: 0.593 AC: 2057 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	1.4
DANN	Benign	0.71
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2265638; hg19: chr10-135217175;