NM_014729.3:c.411+9191T>G

Variant names:

• chr8-58930111-A-C
• rs10504269
• NM_014729.3:c.411+9191T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014729.3(TOX):​c.411+9191T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,952 control chromosomes in the GnomAD database, including 21,404 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 0.53 (21404 hom., cov: 32)
• Consequence: TOX NM_014729.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 9 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TOX	NM_014729.3	c.411+9191T>G		intron_variant	Intron 3 of 8	ENST00000361421.2	NP_055544.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TOX	ENST00000361421.2	c.411+9191T>G		intron_variant	Intron 3 of 8	1	NM_014729.3	ENSP00000354842.1

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80423 AN: 151834 Hom.: 21367 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.506

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.530 AC: 80516 AN: 151952 Hom.: 21404 Cov.: 32 AF XY: 0.528 AC XY: 39225 AN XY: 74272

African (AFR) AF: 0.556 AC: 23016 AN: 41424

American (AMR) AF: 0.540 AC: 8244 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1845 AN: 3470

East Asian (EAS) AF: 0.506 AC: 2614 AN: 5162

South Asian (SAS) AF: 0.391 AC: 1886 AN: 4824

European-Finnish (FIN) AF: 0.564 AC: 5942 AN: 10544

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.517 AC: 35158 AN: 67946

Other (OTH) AF: 0.509 AC: 1075 AN: 2110

Alfa AF: 0.520 Hom.: 34460

Bravo AF: 0.535

Asia WGS AF: 0.504 AC: 1747 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.52
PhyloP100		-0.49
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

Other links and lift over

dbSNP: rs10504269; hg19: chr8-59842670;