chr2-233672130-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_021027.3(UGT1A9):c.196C>T(p.Leu66=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00117 in 1,614,174 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.0062 ( 10 hom., cov: 32)
Exomes 𝑓: 0.00065 ( 16 hom. )
Consequence
UGT1A9
NM_021027.3 synonymous
NM_021027.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.20
Genes affected
UGT1A9 (HGNC:12541): (UDP glucuronosyltransferase family 1 member A9) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The enzyme encoded by this gene is active on phenols. [provided by RefSeq, Jul 2008]
UGT1A10 (HGNC:12531): (UDP glucuronosyltransferase family 1 member A10) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The enzyme encoded by this gene has glucuronidase activity on mycophenolic acid, coumarins, and quinolines. [provided by RefSeq, Jul 2008]
UGT1A8 (HGNC:12540): (UDP glucuronosyltransferase family 1 member A8) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The enzyme encoded by this gene has glucuronidase activity with many substrates including coumarins, phenols, anthraquinones, flavones, and some opioids. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 2-233672130-C-T is Benign according to our data. Variant chr2-233672130-C-T is described in ClinVar as [Benign]. Clinvar id is 3055972.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-1.2 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00618 (942/152334) while in subpopulation AFR AF= 0.021 (874/41566). AF 95% confidence interval is 0.0199. There are 10 homozygotes in gnomad4. There are 464 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 10 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UGT1A9 | NM_021027.3 | c.196C>T | p.Leu66= | synonymous_variant | 1/5 | ENST00000354728.5 | NP_066307.1 | |
UGT1A10 | NM_019075.4 | c.855+34753C>T | intron_variant | ENST00000344644.10 | NP_061948.1 | |||
UGT1A8 | NM_019076.5 | c.855+53568C>T | intron_variant | ENST00000373450.5 | NP_061949.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UGT1A9 | ENST00000354728.5 | c.196C>T | p.Leu66= | synonymous_variant | 1/5 | 1 | NM_021027.3 | ENSP00000346768 | P1 | |
UGT1A10 | ENST00000344644.10 | c.855+34753C>T | intron_variant | 1 | NM_019075.4 | ENSP00000343838 | P1 | |||
UGT1A8 | ENST00000373450.5 | c.855+53568C>T | intron_variant | 1 | NM_019076.5 | ENSP00000362549 | P1 | |||
UGT1A10 | ENST00000373445.1 | c.855+34753C>T | intron_variant | 1 | ENSP00000362544 |
Frequencies
GnomAD3 genomes AF: 0.00620 AC: 944AN: 152216Hom.: 10 Cov.: 32
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GnomAD3 exomes AF: 0.00157 AC: 394AN: 251170Hom.: 3 AF XY: 0.00117 AC XY: 159AN XY: 135710
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GnomAD4 exome AF: 0.000647 AC: 946AN: 1461840Hom.: 16 Cov.: 33 AF XY: 0.000534 AC XY: 388AN XY: 727214
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GnomAD4 genome AF: 0.00618 AC: 942AN: 152334Hom.: 10 Cov.: 32 AF XY: 0.00623 AC XY: 464AN XY: 74490
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
UGT1A9-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 25, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational 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