rs1420529
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001080430.4(TOX3):c.87+21876A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,932 control chromosomes in the GnomAD database, including 25,345 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 0.56 ( 25345 hom., cov: 32)
Consequence
TOX3
NM_001080430.4 intron
NM_001080430.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.225
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOX3 | NM_001080430.4 | c.87+21876A>C | intron_variant | ENST00000219746.14 | |||
TOX3 | NM_001146188.2 | c.-99-5182A>C | intron_variant | ||||
TOX3 | XM_005255892.4 | c.87+21876A>C | intron_variant | ||||
TOX3 | XM_047433909.1 | c.-99-5182A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOX3 | ENST00000219746.14 | c.87+21876A>C | intron_variant | 2 | NM_001080430.4 | A2 | |||
TOX3 | ENST00000407228.7 | c.-99-5182A>C | intron_variant | 2 | P2 | ||||
TOX3 | ENST00000563091.1 | c.-22+22607A>C | intron_variant | 4 | |||||
TOX3 | ENST00000568436.1 | c.87+21876A>C | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.564 AC: 85604AN: 151814Hom.: 25293 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.564 AC: 85718AN: 151932Hom.: 25345 Cov.: 32 AF XY: 0.559 AC XY: 41504AN XY: 74240
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at