rs4771122

chr13-27446043-G-Achr13-27446043-G-Cchr13-27446043-G-T

Variant summary

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

The NM_152912.5(MTIF3):c.-70-887C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 151,472 control chromosomes in the GnomAD database, including 44,262 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 0.76 (44262 hom., cov: 30)
• Consequence: MTIF3 NM_152912.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

Genes affected

MTIF3 (HGNC:29788): (mitochondrial translational initiation factor 3) This gene encodes a translation initiation factor that is involved in mitochondrial protein synthesis. Polymorphism in this gene is associated with the onset of Parkinson's disease. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 5. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTIF3	NM_152912.5	c.-70-887C>T		intron_variant		ENST00000381120.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTIF3	ENST00000381120.8	c.-70-887C>T		intron_variant		1	NM_152912.5	P1

Frequencies

GnomAD3 genomes AF: 0.765 AC: 115739 AN: 151354 Hom.: 44226 Cov.: 30

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.765 AC: 115835 AN: 151472 Hom.: 44262 Cov.: 30 AF XY: 0.757 AC XY: 56058 AN XY: 74014

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.768

Alfa AF: 0.768 Hom.: 49469

Bravo AF: 0.776

Asia WGS AF: 0.738 AC: 2569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.8
Dann	Benign	0.67

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: rs4771122; hg19: chr13-28020180;