rs7284767
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000644773.3(TUG1):c.*2445G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,998 control chromosomes in the GnomAD database, including 13,463 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 0.40 ( 13462 hom., cov: 32)
Exomes 𝑓: 0.75 ( 1 hom. )
Consequence
TUG1
ENST00000644773.3 3_prime_UTR
ENST00000644773.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0280
Genes affected
TUG1 (HGNC:26066): (taurine up-regulated 1) Predicted to act upstream of or within photoreceptor cell development and regulation of gene expression. Predicted to be active in nucleus. Biomarker of Huntington's disease. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.74).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUG1 | NM_001396518.1 | c.*2445G>A | 3_prime_UTR_variant | 2/3 | ENST00000644773.3 | ||
TUG1 | NR_152868.2 | n.731G>A | non_coding_transcript_exon_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUG1 | ENST00000644773.3 | c.*2445G>A | 3_prime_UTR_variant | 2/3 | NM_001396518.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.404 AC: 61365AN: 151876Hom.: 13444 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.750 AC: 3AN: 4Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3AN XY: 4
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GnomAD4 genome ? AF: 0.404 AC: 61423AN: 151994Hom.: 13462 Cov.: 32 AF XY: 0.403 AC XY: 29952AN XY: 74292
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ClinVar
Not reported inComputational scores
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Name
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at