rs753246686
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207377.3(TOMM20L):c.194C>A(p.Thr65Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TOMM20L
NM_207377.3 missense
NM_207377.3 missense
Scores
19
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0720
Genes affected
TOMM20L (HGNC:33752): (translocase of outer mitochondrial membrane 20 like) Predicted to enable mitochondrion targeting sequence binding activity. Predicted to contribute to protein transmembrane transporter activity. Predicted to be involved in protein import into mitochondrial matrix and tRNA import into mitochondrion. Predicted to be integral component of membrane. Predicted to be part of mitochondrial outer membrane translocase complex. Predicted to be integral component of mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.039286405).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| TOMM20L | NM_207377.3 | c.194C>A | p.Thr65Lys | missense_variant | Exon 3 of 5 | ENST00000360945.7 | NP_997260.1 | |
| TOMM20L | XM_011536742.4 | c.218C>A | p.Thr73Lys | missense_variant | Exon 3 of 5 | XP_011535044.1 | ||
| TOMM20L | XM_011536743.3 | c.218C>A | p.Thr73Lys | missense_variant | Exon 3 of 5 | XP_011535045.1 | ||
| TOMM20L | XM_011536744.4 | c.137-4633C>A | intron_variant | Intron 1 of 2 | XP_011535046.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| TOMM20L | ENST00000360945.7 | c.194C>A | p.Thr65Lys | missense_variant | Exon 3 of 5 | 1 | NM_207377.3 | ENSP00000354204.2 | ||
| TOMM20L | ENST00000557754.1 | n.181-4633C>A | intron_variant | Intron 2 of 3 | 1 | ENSP00000451683.1 | ||||
| ENSG00000258378 | ENST00000556734.1 | n.374+3763C>A | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1460798Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 726774
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1460798
Hom.:
Cov.:
29
AF XY:
AC XY:
0
AN XY:
726774
Gnomad4 AFR exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Loss of phosphorylation at T65 (P = 0.0171);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at