rs1885988

Variant names:

• chr13-27436125-T-C
• rs1885988
• NM_152912.5:c.619-232A>G

Variant summary

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

The NM_152912.5(MTIF3):​c.619-232A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,202 control chromosomes in the GnomAD database, including 1,761 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 0.13 (1761 hom., cov: 32)
• Consequence: MTIF3 NM_152912.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 20 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 (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTIF3	NM_152912.5	c.619-232A>G		intron_variant	Intron 4 of 4	ENST00000381120.8	NP_690876.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTIF3	ENST00000381120.8	c.619-232A>G		intron_variant	Intron 4 of 4	1	NM_152912.5	ENSP00000370512.3
MTIF3	ENST00000405591.3	c.619-232A>G		intron_variant	Intron 2 of 2	1		ENSP00000384659.2
MTIF3	ENST00000381116.5	c.619-232A>G		intron_variant	Intron 6 of 6	5		ENSP00000370508.1
MTIF3	ENST00000461838.5	n.738-232A>G		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20182 AN: 152084 Hom.: 1761 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0923

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.133 AC: 20183 AN: 152202 Hom.: 1761 Cov.: 32 AF XY: 0.134 AC XY: 9978 AN XY: 74402

African (AFR) AF: 0.0316 AC: 1313 AN: 41558

American (AMR) AF: 0.111 AC: 1703 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3472

East Asian (EAS) AF: 0.141 AC: 733 AN: 5182

South Asian (SAS) AF: 0.0920 AC: 444 AN: 4826

European-Finnish (FIN) AF: 0.237 AC: 2503 AN: 10556

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12574 AN: 67994

Other (OTH) AF: 0.148 AC: 312 AN: 2112

Alfa AF: 0.167 Hom.: 1308

Bravo AF: 0.119

Asia WGS AF: 0.114 AC: 397 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	1.3
DANN	Benign	0.67
PhyloP100		-0.82
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: rs1885988; hg19: chr13-28010262;