13-27448480-C-T

Variant names:

• chr13-27448480-C-T
• rs17085633
• NM_152912.5:c.-71+2029G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152912.5(MTIF3):​c.-71+2029G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,918 control chromosomes in the GnomAD database, including 13,748 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 0.41 (13748 hom., cov: 32)
• Consequence: MTIF3 NM_152912.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.563 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.-71+2029G>A		intron	N/A	NP_690876.3
	MTIF3	NM_001166261.2		c.-71+1662G>A		intron	N/A	NP_001159733.1	Q9H2K0
	MTIF3	NM_001166262.2		c.-71+1584G>A		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.-71+2029G>A		intron	N/A	ENSP00000370512.3	Q9H2K0
	MTIF3	ENST00000381116.5	TSL:5	c.-113+1372G>A		intron	N/A	ENSP00000370508.1	Q9H2K0
	MTIF3	ENST00000884652.1		c.-2+2029G>A		intron	N/A	ENSP00000554711.1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62200 AN: 151800 Hom.: 13749 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.409 AC: 62201 AN: 151918 Hom.: 13748 Cov.: 32 AF XY: 0.407 AC XY: 30236 AN XY: 74254

African (AFR) AF: 0.273 AC: 11309 AN: 41432

American (AMR) AF: 0.342 AC: 5216 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1907 AN: 3462

East Asian (EAS) AF: 0.233 AC: 1203 AN: 5164

South Asian (SAS) AF: 0.580 AC: 2798 AN: 4820

European-Finnish (FIN) AF: 0.443 AC: 4668 AN: 10530

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33573 AN: 67942

Other (OTH) AF: 0.439 AC: 926 AN: 2110

Alfa AF: 0.426 Hom.: 6247

Bravo AF: 0.390

Asia WGS AF: 0.387 AC: 1346 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.52
PhyloP100		0.024
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: rs17085633; hg19: chr13-28022617;