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GeneBe

rs9921569

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001080430.4(TOX3):c.87+8520A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 32)

Consequence

TOX3
NM_001080430.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.00
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TOX3NM_001080430.4 linkuse as main transcriptc.87+8520A>T intron_variant ENST00000219746.14
TOX3NM_001146188.2 linkuse as main transcriptc.-100+9597A>T intron_variant
TOX3XM_005255892.4 linkuse as main transcriptc.87+8520A>T intron_variant
TOX3XM_047433909.1 linkuse as main transcriptc.-100+8520A>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TOX3ENST00000219746.14 linkuse as main transcriptc.87+8520A>T intron_variant 2 NM_001080430.4 A2O15405-1
TOX3ENST00000407228.7 linkuse as main transcriptc.-100+9597A>T intron_variant 2 P2O15405-2
TOX3ENST00000563091.1 linkuse as main transcriptc.-22+9251A>T intron_variant 4
TOX3ENST00000568436.1 linkuse as main transcriptc.87+8520A>T intron_variant, NMD_transcript_variant 3

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
Cadd
Benign
8.5
Dann
Benign
0.88

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: rs9921569; hg19: chr16-52572029; API