rs564387680

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001128917.2(TOMM40):​c.193G>A​(p.Ala65Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000756 in 1,323,434 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 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: 33)
Exomes 𝑓: 7.6e-7 ( 0 hom. )

Consequence

TOMM40
NM_001128917.2 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.226
Variant links:
Genes affected
TOMM40 (HGNC:18001): (translocase of outer mitochondrial membrane 40) The protein encoded by this gene is localized in the outer membrane of the mitochondria. It is the channel-forming subunit of the translocase of the mitochondrial outer membrane (TOM) complex that is essential for import of protein precursors into mitochondria. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]

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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=0.04855886).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TOMM40NM_001128917.2 linkc.193G>A p.Ala65Thr missense_variant Exon 1 of 9 ENST00000426677.7 NP_001122389.1 O96008-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TOMM40ENST00000426677.7 linkc.193G>A p.Ala65Thr missense_variant Exon 1 of 9 1 NM_001128917.2 ENSP00000410339.1 O96008-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
7.56e-7
AC:
1
AN:
1323434
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
652534
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000344
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.071
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.64
CADD
Benign
12
DANN
Uncertain
0.98
DEOGEN2
Benign
0.070
T;T;.;T;T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.073
N
LIST_S2
Benign
0.43
T;.;T;.;T
M_CAP
Benign
0.0065
T
MetaRNN
Benign
0.049
T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N;N;N;N;.
PrimateAI
Uncertain
0.72
T
PROVEAN
Benign
-0.10
N;N;.;N;.
REVEL
Benign
0.011
Sift
Benign
0.093
T;T;.;T;.
Sift4G
Benign
0.50
T;T;T;T;T
Polyphen
0.0
B;B;B;B;.
Vest4
0.047
MutPred
0.16
Gain of glycosylation at A65 (P = 0.0051);Gain of glycosylation at A65 (P = 0.0051);Gain of glycosylation at A65 (P = 0.0051);Gain of glycosylation at A65 (P = 0.0051);Gain of glycosylation at A65 (P = 0.0051);
MVP
0.10
MPC
0.051
ClinPred
0.061
T
GERP RS
1.7
Varity_R
0.022

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-45394865; API