rs9936081

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080430.4(TOX3):​c.87+30903C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,034 control chromosomes in the GnomAD database, including 7,543 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 0.31 ( 7543 hom., cov: 32)

Consequence

TOX3
NM_001080430.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0340
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TOX3NM_001080430.4 linkuse as main transcriptc.87+30903C>T intron_variant ENST00000219746.14
TOX3NM_001146188.2 linkuse as main transcriptc.75+3672C>T intron_variant
TOX3XM_005255892.4 linkuse as main transcriptc.87+30903C>T intron_variant
TOX3XM_047433909.1 linkuse as main transcriptc.75+3672C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TOX3ENST00000219746.14 linkuse as main transcriptc.87+30903C>T intron_variant 2 NM_001080430.4 A2O15405-1
TOX3ENST00000407228.7 linkuse as main transcriptc.75+3672C>T intron_variant 2 P2O15405-2
TOX3ENST00000563091.1 linkuse as main transcriptc.-22+31634C>T intron_variant 4
TOX3ENST00000568436.1 linkuse as main transcriptc.87+30903C>T intron_variant, NMD_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.310
AC:
47113
AN:
151916
Hom.:
7528
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.385
Gnomad AMI
AF:
0.307
Gnomad AMR
AF:
0.309
Gnomad ASJ
AF:
0.370
Gnomad EAS
AF:
0.416
Gnomad SAS
AF:
0.215
Gnomad FIN
AF:
0.291
Gnomad MID
AF:
0.329
Gnomad NFE
AF:
0.263
Gnomad OTH
AF:
0.305
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.310
AC:
47168
AN:
152034
Hom.:
7543
Cov.:
32
AF XY:
0.311
AC XY:
23126
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.385
Gnomad4 AMR
AF:
0.309
Gnomad4 ASJ
AF:
0.370
Gnomad4 EAS
AF:
0.415
Gnomad4 SAS
AF:
0.215
Gnomad4 FIN
AF:
0.291
Gnomad4 NFE
AF:
0.263
Gnomad4 OTH
AF:
0.309
Alfa
AF:
0.284
Hom.:
2661
Bravo
AF:
0.319
Asia WGS
AF:
0.301
AC:
1049
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
3.1
DANN
Benign
0.76

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: rs9936081; hg19: chr16-52549646; API