chr12-109543873-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_011538961.2(UBE3B):c.*260C>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 0.567 in 151,772 control chromosomes in the GnomAD database, including 25,410 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 0.57 ( 25410 hom., cov: 29)
Consequence
UBE3B
XM_011538961.2 3_prime_UTR
XM_011538961.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.668
Genes affected
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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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBE3B | XM_011538961.2 | c.*260C>T | 3_prime_UTR_variant | 28/28 | |||
UBE3B | XM_047429851.1 | c.*260C>T | 3_prime_UTR_variant | 28/28 | |||
UBE3B | XM_047429852.1 | c.*260C>T | 3_prime_UTR_variant | 28/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes AF: 0.567 AC: 85953AN: 151658Hom.: 25369 Cov.: 29
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.567 AC: 86055AN: 151772Hom.: 25410 Cov.: 29 AF XY: 0.557 AC XY: 41308AN XY: 74168
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at