8-58878344-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014729.3(TOX):c.412-26539A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,174 control chromosomes in the GnomAD database, including 3,553 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 0.20 ( 3553 hom., cov: 32)
Consequence
TOX
NM_014729.3 intron
NM_014729.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.16
Genes affected
TOX (HGNC:18988): (thymocyte selection associated high mobility group box) The protein encoded by this gene contains a HMG box DNA binding domain. HMG boxes are found in many eukaryotic proteins involved in chromatin assembly, transcription and replication. This protein may function to regulate T-cell development.[provided by RefSeq, Apr 2009]
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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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.205 AC: 31150AN: 152056Hom.: 3550 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
31150
AN:
152056
Hom.:
Cov.:
32
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.205 AC: 31171AN: 152174Hom.: 3553 Cov.: 32 AF XY: 0.202 AC XY: 15007AN XY: 74408 show subpopulations
GnomAD4 genome
AF:
AC:
31171
AN:
152174
Hom.:
Cov.:
32
AF XY:
AC XY:
15007
AN XY:
74408
show subpopulations
African (AFR)
AF:
AC:
12020
AN:
41510
American (AMR)
AF:
AC:
2627
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
1033
AN:
3466
East Asian (EAS)
AF:
AC:
288
AN:
5190
South Asian (SAS)
AF:
AC:
1079
AN:
4828
European-Finnish (FIN)
AF:
AC:
1476
AN:
10594
Middle Eastern (MID)
AF:
AC:
62
AN:
294
European-Non Finnish (NFE)
AF:
AC:
12146
AN:
67984
Other (OTH)
AF:
AC:
401
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1248
2496
3743
4991
6239
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
560
AN:
3474
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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