rs1885988

Positions:

• chr13-27436125-T-C

Variant summary

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

The ENST00000381120.8(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 ENST00000381120.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818

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=-0.89).
• 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/exons	MANE	Protein	UniProt
MTIF3	NM_152912.5	c.619-232A>G		intron_variant		ENST00000381120.8	NP_690876.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTIF3	ENST00000381120.8	c.619-232A>G		intron_variant		1	NM_152912.5	ENSP00000370512	P1
MTIF3	ENST00000405591.3	c.619-232A>G		intron_variant		1		ENSP00000384659	P1
MTIF3	ENST00000381116.5	c.619-232A>G		intron_variant		5		ENSP00000370508	P1
MTIF3	ENST00000461838.5	n.738-232A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0316

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0920

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.148

Alfa AF: 0.168 Hom.: 1195

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

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: rs1885988; hg19: chr13-28010262;