19-44901434-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -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
NM_001128917.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.31
Publications
48 publications found
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 was made for transcript
Our verdict: Benign. The variant received -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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.764 AC: 116208AN: 152096Hom.: 45058 Cov.: 34 show subpopulations
GnomAD3 genomes
AF:
AC:
116208
AN:
152096
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.721 AC: 968433AN: 1342278Hom.: 351926 Cov.: 52 AF XY: 0.720 AC XY: 471340AN XY: 654762 show subpopulations
GnomAD4 exome
AF:
AC:
968433
AN:
1342278
Hom.:
Cov.:
52
AF XY:
AC XY:
471340
AN XY:
654762
show subpopulations
African (AFR)
AF:
AC:
26668
AN:
30234
American (AMR)
AF:
AC:
22035
AN:
29718
Ashkenazi Jewish (ASJ)
AF:
AC:
17318
AN:
21484
East Asian (EAS)
AF:
AC:
15745
AN:
35144
South Asian (SAS)
AF:
AC:
46546
AN:
71182
European-Finnish (FIN)
AF:
AC:
35646
AN:
45382
Middle Eastern (MID)
AF:
AC:
4167
AN:
5394
European-Non Finnish (NFE)
AF:
AC:
761012
AN:
1048312
Other (OTH)
AF:
AC:
39296
AN:
55428
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.489
Heterozygous variant carriers
0
14410
28820
43229
57639
72049
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
19588
39176
58764
78352
97940
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.764 AC: 116336AN: 152214Hom.: 45120 Cov.: 34 AF XY: 0.764 AC XY: 56850AN XY: 74422 show subpopulations
GnomAD4 genome
AF:
AC:
116336
AN:
152214
Hom.:
Cov.:
34
AF XY:
AC XY:
56850
AN XY:
74422
show subpopulations
African (AFR)
AF:
AC:
36409
AN:
41554
American (AMR)
AF:
AC:
11134
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
2816
AN:
3472
East Asian (EAS)
AF:
AC:
2214
AN:
5166
South Asian (SAS)
AF:
AC:
3129
AN:
4818
European-Finnish (FIN)
AF:
AC:
8357
AN:
10604
Middle Eastern (MID)
AF:
AC:
229
AN:
294
European-Non Finnish (NFE)
AF:
AC:
49727
AN:
68000
Other (OTH)
AF:
AC:
1598
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1413
2827
4240
5654
7067
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
850
1700
2550
3400
4250
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2170
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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