chr8-58878344-T-C

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TOXNM_014729.3 linkc.412-26539A>G intron_variant Intron 3 of 8 ENST00000361421.2 NP_055544.1 O94900

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TOXENST00000361421.2 linkc.412-26539A>G intron_variant Intron 3 of 8 1 NM_014729.3 ENSP00000354842.1 O94900

Frequencies

GnomAD3 genomes
AF:
0.205
AC:
31150
AN:
152056
Hom.:
3550
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.290
Gnomad AMI
AF:
0.0428
Gnomad AMR
AF:
0.172
Gnomad ASJ
AF:
0.298
Gnomad EAS
AF:
0.0554
Gnomad SAS
AF:
0.225
Gnomad FIN
AF:
0.139
Gnomad MID
AF:
0.206
Gnomad NFE
AF:
0.179
Gnomad OTH
AF:
0.192
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.205
AC:
31171
AN:
152174
Hom.:
3553
Cov.:
32
AF XY:
0.202
AC XY:
15007
AN XY:
74408
show subpopulations
African (AFR)
AF:
0.290
AC:
12020
AN:
41510
American (AMR)
AF:
0.172
AC:
2627
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.298
AC:
1033
AN:
3466
East Asian (EAS)
AF:
0.0555
AC:
288
AN:
5190
South Asian (SAS)
AF:
0.223
AC:
1079
AN:
4828
European-Finnish (FIN)
AF:
0.139
AC:
1476
AN:
10594
Middle Eastern (MID)
AF:
0.211
AC:
62
AN:
294
European-Non Finnish (NFE)
AF:
0.179
AC:
12146
AN:
67984
Other (OTH)
AF:
0.190
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

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
326
652
978
1304
1630
<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:
0.187
Hom.:
391
Bravo
AF:
0.207
Asia WGS
AF:
0.161
AC:
560
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.97
DANN
Benign
0.74
PhyloP100
-1.2
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs765587; hg19: chr8-59790903; API