GeneBe

rs10524523

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001128917.2(TOMM40):​c.644-926_644-904delTTTTTTTTTTTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)
Failed GnomAD Quality Control

Consequence

TOMM40
NM_001128917.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.499

Publications

124 publications found
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 was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001128917.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TOMM40
NM_001128917.2
MANE Select
c.644-926_644-904delTTTTTTTTTTTTTTTTTTTTTTT
intron
N/ANP_001122389.1O96008-1
TOMM40
NM_001128916.2
c.644-926_644-904delTTTTTTTTTTTTTTTTTTTTTTT
intron
N/ANP_001122388.1O96008-1
TOMM40
NM_006114.3
c.644-926_644-904delTTTTTTTTTTTTTTTTTTTTTTT
intron
N/ANP_006105.1O96008-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TOMM40
ENST00000426677.7
TSL:1 MANE Select
c.644-938_644-916delTTTTTTTTTTTTTTTTTTTTTTT
intron
N/AENSP00000410339.1O96008-1
TOMM40
ENST00000252487.9
TSL:1
c.644-938_644-916delTTTTTTTTTTTTTTTTTTTTTTT
intron
N/AENSP00000252487.4O96008-1
TOMM40
ENST00000405636.6
TSL:1
c.644-938_644-916delTTTTTTTTTTTTTTTTTTTTTTT
intron
N/AENSP00000385184.2O96008-1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
90982
Hom.:
0
Cov.:
0
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
90982
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
41714
African (AFR)
AF:
0.00
AC:
0
AN:
26920
American (AMR)
AF:
0.00
AC:
0
AN:
6792
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2398
East Asian (EAS)
AF:
0.00
AC:
0
AN:
2398
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2182
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
3312
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
138
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
44964
Other (OTH)
AF:
0.00
AC:
0
AN:
1228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs10524523; hg19: chr19-45403048; API