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GeneBe

rs405697

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001128917.2(TOMM40):c.946+124A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 1,494,492 control chromosomes in the GnomAD database, including 397,046 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 0.76 ( 45120 hom., cov: 34)
Exomes 𝑓: 0.72 ( 351926 hom. )

Consequence

TOMM40
NM_001128917.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.31
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TOMM40NM_001128917.2 linkuse as main transcriptc.946+124A>G intron_variant ENST00000426677.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TOMM40ENST00000426677.7 linkuse as main transcriptc.946+124A>G intron_variant 1 NM_001128917.2 P1O96008-1

Frequencies

GnomAD3 genomes
AF:
0.764
AC:
116208
AN:
152096
Hom.:
45058
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.876
Gnomad AMI
AF:
0.796
Gnomad AMR
AF:
0.728
Gnomad ASJ
AF:
0.811
Gnomad EAS
AF:
0.428
Gnomad SAS
AF:
0.648
Gnomad FIN
AF:
0.788
Gnomad MID
AF:
0.788
Gnomad NFE
AF:
0.731
Gnomad OTH
AF:
0.755
GnomAD4 exome
AF:
0.721
AC:
968433
AN:
1342278
Hom.:
351926
Cov.:
52
AF XY:
0.720
AC XY:
471340
AN XY:
654762
show subpopulations
Gnomad4 AFR exome
AF:
0.882
Gnomad4 AMR exome
AF:
0.741
Gnomad4 ASJ exome
AF:
0.806
Gnomad4 EAS exome
AF:
0.448
Gnomad4 SAS exome
AF:
0.654
Gnomad4 FIN exome
AF:
0.785
Gnomad4 NFE exome
AF:
0.726
Gnomad4 OTH exome
AF:
0.709
GnomAD4 genome
AF:
0.764
AC:
116336
AN:
152214
Hom.:
45120
Cov.:
34
AF XY:
0.764
AC XY:
56850
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.876
Gnomad4 AMR
AF:
0.728
Gnomad4 ASJ
AF:
0.811
Gnomad4 EAS
AF:
0.429
Gnomad4 SAS
AF:
0.649
Gnomad4 FIN
AF:
0.788
Gnomad4 NFE
AF:
0.731
Gnomad4 OTH
AF:
0.757
Alfa
AF:
0.741
Hom.:
32593
Bravo
AF:
0.763
Asia WGS
AF:
0.624
AC:
2170
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
12
Dann
Benign
0.21

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.19
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs405697; hg19: chr19-45404691; COSMIC: COSV52986417; COSMIC: COSV52986417; API