16-52538117-T-C

Variant names:

• chr16-52538117-T-C
• rs9921569
• NM_001080430.4:c.87+8520A>G

Variant summary

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

The NM_001080430.4(TOX3):​c.87+8520A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,956 control chromosomes in the GnomAD database, including 7,951 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 0.32 (7951 hom., cov: 32)
• Consequence: TOX3 NM_001080430.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 3 publications found

Genes affected

TOX3 (HGNC:11972): (TOX high mobility group box family member 3) The protein encoded by this gene contains an HMG-box, indicating that it may be involved in bending and unwinding of DNA and alteration of chromatin structure. The C-terminus of the encoded protein is glutamine-rich due to CAG repeats in the coding sequence. A minor allele of this gene has been implicated in an elevated risk of breast cancer. Two transcript variants encoding different isoforms have been found for this gene.[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=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080430.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOX3	NM_001080430.4	MANE Select	c.87+8520A>G		intron	N/A	NP_001073899.2	O15405-1
	TOX3	NM_001146188.2		c.-100+9597A>G		intron	N/A	NP_001139660.1	O15405-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOX3	ENST00000219746.14	TSL:2 MANE Select	c.87+8520A>G		intron	N/A	ENSP00000219746.9	O15405-1
	TOX3	ENST00000912163.1		c.87+8520A>G		intron	N/A	ENSP00000582222.1
	TOX3	ENST00000873102.1		c.87+8520A>G		intron	N/A	ENSP00000543161.1

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48207 AN: 151840 Hom.: 7939 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.318 AC: 48265 AN: 151956 Hom.: 7951 Cov.: 32 AF XY: 0.320 AC XY: 23761 AN XY: 74294

African (AFR) AF: 0.384 AC: 15906 AN: 41422

American (AMR) AF: 0.358 AC: 5457 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3470

East Asian (EAS) AF: 0.465 AC: 2403 AN: 5168

South Asian (SAS) AF: 0.219 AC: 1055 AN: 4810

European-Finnish (FIN) AF: 0.294 AC: 3105 AN: 10554

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18000 AN: 67964

Other (OTH) AF: 0.320 AC: 676 AN: 2110

Alfa AF: 0.288 Hom.: 4237

Bravo AF: 0.329

Asia WGS AF: 0.334 AC: 1159 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.8
DANN	Benign	0.86
PhyloP100		1.0
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: rs9921569; hg19: chr16-52572029;