4-68646936-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001076.4(UGT2B15):c.*168C>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 0.5 in 149,736 control chromosomes in the GnomAD database, including 21,322 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 0.50 ( 21322 hom., cov: 31)
Exomes 𝑓: 0.61 ( 163336 hom. )
Failed GnomAD Quality Control
Consequence
UGT2B15
NM_001076.4 3_prime_UTR
NM_001076.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.07
Genes affected
UGT2B15 (HGNC:12546): (UDP glucuronosyltransferase family 2 member B15) This gene encodes a glycosyltransferase that is invovled in the metabolism and elimination of toxic compounts, both endogenous and of xenobiotic origin. This gene plays a role in the regulation of estrogens and androgens. This locus is present in a cluster of similar genes and pseudogenes on chromosome 4. [provided by RefSeq, Aug 2016]
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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=-1.03).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UGT2B15 | NM_001076.4 | c.*168C>T | 3_prime_UTR_variant | 6/6 | ENST00000338206.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UGT2B15 | ENST00000338206.6 | c.*168C>T | 3_prime_UTR_variant | 6/6 | 1 | NM_001076.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.500 AC: 74850AN: 149624Hom.: 21320 Cov.: 31
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.612 AC: 520726AN: 851552Hom.: 163336 Cov.: 11 AF XY: 0.610 AC XY: 260089AN XY: 426426
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.500 AC: 74879AN: 149736Hom.: 21322 Cov.: 31 AF XY: 0.498 AC XY: 36364AN XY: 73016
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at