rs10022440
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001074.4(UGT2B7):c.1091-95G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0675 in 1,471,668 control chromosomes in the GnomAD database, including 3,767 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 0.062 ( 349 hom., cov: 32)
Exomes 𝑓: 0.068 ( 3418 hom. )
Consequence
UGT2B7
NM_001074.4 intron
NM_001074.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.378
Genes affected
UGT2B7 (HGNC:12554): (UDP glucuronosyltransferase family 2 member B7) The protein encoded by this gene belongs to the UDP-glycosyltransferase (UGT) family. UGTs serve a major role in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This protein is localized in the microsome membrane, and has unique specificity for 3,4-catechol estrogens and estriol, suggesting that it may play an important role in regulating the level and activity of these potent estrogen metabolites. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2017]
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0748 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UGT2B7 | NM_001074.4 | c.1091-95G>A | intron_variant | ENST00000305231.12 | |||
UGT2B7 | NM_001330719.2 | c.1090+746G>A | intron_variant | ||||
UGT2B7 | NM_001349568.2 | c.344-95G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UGT2B7 | ENST00000305231.12 | c.1091-95G>A | intron_variant | 1 | NM_001074.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0617 AC: 9383AN: 152084Hom.: 348 Cov.: 32
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GnomAD4 exome AF: 0.0682 AC: 89984AN: 1319466Hom.: 3418 AF XY: 0.0668 AC XY: 44262AN XY: 662162
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GnomAD4 genome ? AF: 0.0617 AC: 9386AN: 152202Hom.: 349 Cov.: 32 AF XY: 0.0597 AC XY: 4442AN XY: 74408
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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