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GeneBe

rs2075650

Variant summary

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

The NM_001128917.2(TOMM40):c.275-31A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,608,116 control chromosomes in the GnomAD database, including 16,065 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 0.13 ( 1342 hom., cov: 32)
Exomes 𝑓: 0.14 ( 14723 hom. )

Consequence

TOMM40
NM_001128917.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03
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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TOMM40NM_001128917.2 linkuse as main transcriptc.275-31A>G intron_variant ENST00000426677.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TOMM40ENST00000426677.7 linkuse as main transcriptc.275-31A>G intron_variant 1 NM_001128917.2 P1O96008-1

Frequencies

GnomAD3 genomes
AF:
0.132
AC:
20043
AN:
151888
Hom.:
1333
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.129
Gnomad AMI
AF:
0.144
Gnomad AMR
AF:
0.105
Gnomad ASJ
AF:
0.114
Gnomad EAS
AF:
0.108
Gnomad SAS
AF:
0.122
Gnomad FIN
AF:
0.172
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.138
Gnomad OTH
AF:
0.0970
GnomAD3 exomes
AF:
0.129
AC:
32485
AN:
251370
Hom.:
2148
AF XY:
0.129
AC XY:
17530
AN XY:
135868
show subpopulations
Gnomad AFR exome
AF:
0.124
Gnomad AMR exome
AF:
0.0978
Gnomad ASJ exome
AF:
0.104
Gnomad EAS exome
AF:
0.0865
Gnomad SAS exome
AF:
0.116
Gnomad FIN exome
AF:
0.182
Gnomad NFE exome
AF:
0.143
Gnomad OTH exome
AF:
0.122
GnomAD4 exome
AF:
0.141
AC:
205242
AN:
1456110
Hom.:
14723
Cov.:
30
AF XY:
0.141
AC XY:
101870
AN XY:
724748
show subpopulations
Gnomad4 AFR exome
AF:
0.124
Gnomad4 AMR exome
AF:
0.0984
Gnomad4 ASJ exome
AF:
0.111
Gnomad4 EAS exome
AF:
0.129
Gnomad4 SAS exome
AF:
0.118
Gnomad4 FIN exome
AF:
0.175
Gnomad4 NFE exome
AF:
0.146
Gnomad4 OTH exome
AF:
0.125
GnomAD4 genome
AF:
0.132
AC:
20086
AN:
152006
Hom.:
1342
Cov.:
32
AF XY:
0.133
AC XY:
9904
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.129
Gnomad4 AMR
AF:
0.106
Gnomad4 ASJ
AF:
0.114
Gnomad4 EAS
AF:
0.108
Gnomad4 SAS
AF:
0.121
Gnomad4 FIN
AF:
0.172
Gnomad4 NFE
AF:
0.138
Gnomad4 OTH
AF:
0.103
Alfa
AF:
0.129
Hom.:
3069
Bravo
AF:
0.124
Asia WGS
AF:
0.172
AC:
598
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
2.5
Dann
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs2075650; hg19: chr19-45395619; COSMIC: COSV52977687; COSMIC: COSV52977687; API