rs851800

chr8-59026623-A-Cchr8-59026623-A-Gchr8-59026623-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014729.3(TOX):c.103-66615T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 152,090 control chromosomes in the GnomAD database, including 54,586 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 0.84 (54586 hom., cov: 30)
• Consequence: TOX NM_014729.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TOX	NM_014729.3	c.103-66615T>G		intron_variant		ENST00000361421.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TOX	ENST00000361421.2	c.103-66615T>G		intron_variant		1	NM_014729.3	P1

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128271 AN: 151972 Hom.: 54558 Cov.: 30

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.844 AC: 128352 AN: 152090 Hom.: 54586 Cov.: 30 AF XY: 0.848 AC XY: 63007 AN XY: 74342

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.895

Gnomad4 NFE AF: 0.870

Gnomad4 OTH AF: 0.840

Alfa AF: 0.861 Hom.: 50501

Bravo AF: 0.839

Asia WGS AF: 0.947 AC: 3293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	16
Dann	Benign	0.85

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

Other links and lift over

dbSNP: rs851800; hg19: chr8-59939182;