rs4771122

Variant names:

• chr13-27446043-G-A
• rs4771122
• NM_152912.5:c.-70-887C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-27446043-G-A
• chr13-27446043-G-C
• chr13-27446043-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 132 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152912.5. 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
	MTIF3	NM_152912.5	MANE Select	c.-70-887C>T		intron	N/A	NP_690876.3
	MTIF3	NM_001166261.2		c.-70-887C>T		intron	N/A	NP_001159733.1	Q9H2K0
	MTIF3	NM_001166262.2		c.-70-887C>T		intron	N/A	NP_001159734.1	Q9H2K0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTIF3	ENST00000381120.8	TSL:1 MANE Select	c.-70-887C>T		intron	N/A	ENSP00000370512.3	Q9H2K0
	MTIF3	ENST00000381116.5	TSL:5	c.-112-906C>T		intron	N/A	ENSP00000370508.1	Q9H2K0
	MTIF3	ENST00000884652.1		c.-2+4466C>T		intron	N/A	ENSP00000554711.1

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

African (AFR) AF: 0.781 AC: 32250 AN: 41284

American (AMR) AF: 0.783 AC: 11921 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2742 AN: 3466

East Asian (EAS) AF: 0.788 AC: 4065 AN: 5160

South Asian (SAS) AF: 0.771 AC: 3701 AN: 4802

European-Finnish (FIN) AF: 0.644 AC: 6714 AN: 10426

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 51922 AN: 67816

Other (OTH) AF: 0.768 AC: 1611 AN: 2098

Alfa AF: 0.765 Hom.: 122640

Bravo AF: 0.776

Asia WGS AF: 0.738 AC: 2569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.67
PhyloP100		-0.032
Mutation Taster		=100/0	polymorphism (auto)

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: rs4771122; hg19: chr13-28020180;