rs10857712

Positions:

• chr10-133412162-T-C

Variant summary

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

The NM_138384.4(MTG1):​c.753-7318T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,008 control chromosomes in the GnomAD database, including 4,772 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 0.25 (4772 hom., cov: 32)
• Consequence: MTG1 NM_138384.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

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]

ENSG00000254536 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTG1	NM_138384.4	c.753-7318T>C		intron_variant		ENST00000317502.11	NP_612393.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTG1	ENST00000317502.11	c.753-7318T>C		intron_variant		1	NM_138384.4	ENSP00000323047.6
MTG1	ENST00000477902.6	c.630-7318T>C		intron_variant		3		ENSP00000475596.1
ENSG00000254536	ENST00000468317.3	n.*677-7318T>C		intron_variant		5		ENSP00000436767.2

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37314 AN: 151890 Hom.: 4766 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.246 AC: 37322 AN: 152008 Hom.: 4772 Cov.: 32 AF XY: 0.248 AC XY: 18430 AN XY: 74312

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.244

Alfa AF: 0.228 Hom.: 6309

Bravo AF: 0.256

Asia WGS AF: 0.267 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.0
DANN	Benign	0.96
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Publications

LitVar

Other links and lift over

dbSNP: rs10857712; hg19: chr10-135225666;