chr16-52439807-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001080430.4(TOX3):c.1149C>T(p.Ile383=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000815 in 1,613,910 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0045 ( 6 hom., cov: 32)
Exomes 𝑓: 0.00044 ( 2 hom. )
Consequence
TOX3
NM_001080430.4 synonymous
NM_001080430.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.03
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
?
Variant 16-52439807-G-A is Benign according to our data. Variant chr16-52439807-G-A is described in ClinVar as [Benign]. Clinvar id is 777016.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.03 with no splicing effect.
BS2
?
High AC in GnomAd at 668 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOX3 | NM_001080430.4 | c.1149C>T | p.Ile383= | synonymous_variant | 7/7 | ENST00000219746.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOX3 | ENST00000219746.14 | c.1149C>T | p.Ile383= | synonymous_variant | 7/7 | 2 | NM_001080430.4 | A2 | |
TOX3 | ENST00000407228.7 | c.1134C>T | p.Ile378= | synonymous_variant | 8/8 | 2 | P2 | ||
TOX3 | ENST00000566696.1 | n.1613C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00439 AC: 668AN: 152088Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00118 AC: 295AN: 249286Hom.: 3 AF XY: 0.000821 AC XY: 111AN XY: 135244
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GnomAD4 exome AF: 0.000436 AC: 638AN: 1461704Hom.: 2 Cov.: 33 AF XY: 0.000385 AC XY: 280AN XY: 727134
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at