rs12545204

Variant summary

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

The ENST00000361421.2(TOX):​c.103-13745A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,066 control chromosomes in the GnomAD database, including 40,581 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 0.72 ( 40581 hom., cov: 31)

Consequence

TOX
ENST00000361421.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.279
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TOXNM_014729.3 linkuse as main transcriptc.103-13745A>T intron_variant ENST00000361421.2 NP_055544.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TOXENST00000361421.2 linkuse as main transcriptc.103-13745A>T intron_variant 1 NM_014729.3 ENSP00000354842 P1

Frequencies

GnomAD3 genomes
AF:
0.725
AC:
110122
AN:
151948
Hom.:
40561
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.590
Gnomad AMI
AF:
0.791
Gnomad AMR
AF:
0.688
Gnomad ASJ
AF:
0.795
Gnomad EAS
AF:
0.726
Gnomad SAS
AF:
0.825
Gnomad FIN
AF:
0.842
Gnomad MID
AF:
0.685
Gnomad NFE
AF:
0.786
Gnomad OTH
AF:
0.714
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.725
AC:
110190
AN:
152066
Hom.:
40581
Cov.:
31
AF XY:
0.728
AC XY:
54093
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.590
Gnomad4 AMR
AF:
0.688
Gnomad4 ASJ
AF:
0.795
Gnomad4 EAS
AF:
0.726
Gnomad4 SAS
AF:
0.826
Gnomad4 FIN
AF:
0.842
Gnomad4 NFE
AF:
0.785
Gnomad4 OTH
AF:
0.717
Alfa
AF:
0.745
Hom.:
5039
Bravo
AF:
0.702
Asia WGS
AF:
0.760
AC:
2642
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
1.4
DANN
Benign
0.84

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12545204; hg19: chr8-59886312; API