chr1-10130826-A-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001105562.3(UBE4B):c.1911+13A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 1,609,586 control chromosomes in the GnomAD database, including 134,203 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 0.47 ( 17539 hom., cov: 32)
Exomes 𝑓: 0.40 ( 116664 hom. )
Consequence
UBE4B
NM_001105562.3 intron
NM_001105562.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.50
Genes affected
UBE4B (HGNC:12500): (ubiquitination factor E4B) The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes an additional conjugation factor, E4, which is involved in multiubiquitin chain assembly. This gene is also the strongest candidate in the neuroblastoma tumor suppressor genes. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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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=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBE4B | NM_001105562.3 | c.1911+13A>T | intron_variant | ENST00000343090.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBE4B | ENST00000343090.11 | c.1911+13A>T | intron_variant | 1 | NM_001105562.3 |
Frequencies
GnomAD3 genomes AF: 0.465 AC: 70648AN: 151932Hom.: 17509 Cov.: 32
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GnomAD3 exomes AF: 0.420 AC: 105097AN: 250144Hom.: 22859 AF XY: 0.410 AC XY: 55418AN XY: 135170
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GnomAD4 exome AF: 0.397 AC: 578047AN: 1457536Hom.: 116664 Cov.: 31 AF XY: 0.395 AC XY: 286240AN XY: 725354
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GnomAD4 genome AF: 0.465 AC: 70727AN: 152050Hom.: 17539 Cov.: 32 AF XY: 0.462 AC XY: 34314AN XY: 74316
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at