rs4755
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006472.6(TXNIP):c.*1045A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,516 control chromosomes in the GnomAD database, including 3,264 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 0.15 ( 3262 hom., cov: 32)
Exomes 𝑓: 0.064 ( 2 hom. )
Consequence
TXNIP
NM_006472.6 3_prime_UTR
NM_006472.6 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.13
Genes affected
TXNIP (HGNC:16952): (thioredoxin interacting protein) This gene encodes a thioredoxin-binding protein that is a member of the alpha arrestin protein family. Thioredoxin is a thiol-oxidoreductase that is a major regulator of cellular redox signaling which protects cells from oxidative stress. This protein inhibits the antioxidative function of thioredoxin resulting in the accumulation of reactive oxygen species and cellular stress. This protein also functions as a regulator of cellular metabolism and of endoplasmic reticulum (ER) stress. This protein may also function as a tumor suppressor. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
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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 (Cadd=10.32).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNIP | NM_006472.6 | c.*1045A>T | 3_prime_UTR_variant | 8/8 | ENST00000582401.6 | ||
TXNIP | NM_001313972.2 | c.*1045A>T | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNIP | ENST00000582401.6 | c.*1045A>T | 3_prime_UTR_variant | 8/8 | 1 | NM_006472.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.153 AC: 23202AN: 151926Hom.: 3245 Cov.: 32
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GnomAD4 exome AF: 0.0636 AC: 30AN: 472Hom.: 2 Cov.: 0 AF XY: 0.0646 AC XY: 19AN XY: 294
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GnomAD4 genome ? AF: 0.153 AC: 23259AN: 152044Hom.: 3262 Cov.: 32 AF XY: 0.154 AC XY: 11484AN XY: 74362
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ClinVar
Not reported inComputational scores
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Score
Prediction
CADD
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at