rs140262959
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The ENST00000381120.8(MTIF3):āc.413A>Gā(p.Gln138Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00979 in 1,614,238 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0072 ( 7 hom., cov: 32)
Exomes š: 0.010 ( 88 hom. )
Consequence
MTIF3
ENST00000381120.8 missense
ENST00000381120.8 missense
Scores
1
4
13
Clinical Significance
Conservation
PhyloP100: 5.84
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.007491678).
BP6
Variant 13-27440036-T-C is Benign according to our data. Variant chr13-27440036-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 445609.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-27440036-T-C is described in Lovd as [Likely_benign].
BS2
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTIF3 | NM_152912.5 | c.413A>G | p.Gln138Arg | missense_variant | 3/5 | ENST00000381120.8 | NP_690876.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTIF3 | ENST00000381120.8 | c.413A>G | p.Gln138Arg | missense_variant | 3/5 | 1 | NM_152912.5 | ENSP00000370512 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00725 AC: 1103AN: 152228Hom.: 7 Cov.: 32
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GnomAD3 exomes AF: 0.00772 AC: 1941AN: 251482Hom.: 13 AF XY: 0.00801 AC XY: 1089AN XY: 135912
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GnomAD4 exome AF: 0.0101 AC: 14706AN: 1461892Hom.: 88 Cov.: 32 AF XY: 0.0100 AC XY: 7269AN XY: 727246
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GnomAD4 genome AF: 0.00723 AC: 1102AN: 152346Hom.: 7 Cov.: 32 AF XY: 0.00701 AC XY: 522AN XY: 74504
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 15, 2017 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
.;.;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
P;P;P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at