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GeneBe

rs157580

Variant summary

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

The NM_001128917.2(TOMM40):c.274+320G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 151,936 control chromosomes in the GnomAD database, including 36,886 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 0.69 ( 36886 hom., cov: 31)

Consequence

TOMM40
NM_001128917.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.596
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TOMM40NM_001128917.2 linkuse as main transcriptc.274+320G>A intron_variant ENST00000426677.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TOMM40ENST00000426677.7 linkuse as main transcriptc.274+320G>A intron_variant 1 NM_001128917.2 P1O96008-1

Frequencies

GnomAD3 genomes
AF:
0.687
AC:
104279
AN:
151818
Hom.:
36820
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.853
Gnomad AMI
AF:
0.686
Gnomad AMR
AF:
0.674
Gnomad ASJ
AF:
0.624
Gnomad EAS
AF:
0.455
Gnomad SAS
AF:
0.538
Gnomad FIN
AF:
0.732
Gnomad MID
AF:
0.528
Gnomad NFE
AF:
0.615
Gnomad OTH
AF:
0.653
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.687
AC:
104414
AN:
151936
Hom.:
36886
Cov.:
31
AF XY:
0.692
AC XY:
51363
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.853
Gnomad4 AMR
AF:
0.674
Gnomad4 ASJ
AF:
0.624
Gnomad4 EAS
AF:
0.457
Gnomad4 SAS
AF:
0.538
Gnomad4 FIN
AF:
0.732
Gnomad4 NFE
AF:
0.615
Gnomad4 OTH
AF:
0.656
Alfa
AF:
0.617
Hom.:
62693
Bravo
AF:
0.689

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
4.4
Dann
Benign
0.83

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs157580; hg19: chr19-45395266; API