chr2-233672434-T-C

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_021027.3(UGT1A9):ā€‹c.500T>Cā€‹(p.Val167Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000929 in 1,613,976 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: š‘“ 0.0010 ( 1 hom., cov: 32)
Exomes š‘“: 0.00092 ( 3 hom. )

Consequence

UGT1A9
NM_021027.3 missense

Scores

1
17

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.52
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.016549855).
BP6
Variant 2-233672434-T-C is Benign according to our data. Variant chr2-233672434-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3046264.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High Homozygotes in GnomAdExome4 at 3 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
UGT1A9NM_021027.3 linkuse as main transcriptc.500T>C p.Val167Ala missense_variant 1/5 ENST00000354728.5 NP_066307.1
UGT1A10NM_019075.4 linkuse as main transcriptc.855+35057T>C intron_variant ENST00000344644.10 NP_061948.1
UGT1A8NM_019076.5 linkuse as main transcriptc.855+53872T>C intron_variant ENST00000373450.5 NP_061949.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UGT1A9ENST00000354728.5 linkuse as main transcriptc.500T>C p.Val167Ala missense_variant 1/51 NM_021027.3 ENSP00000346768 P1O60656-1
UGT1A10ENST00000344644.10 linkuse as main transcriptc.855+35057T>C intron_variant 1 NM_019075.4 ENSP00000343838 P1Q9HAW8-1
UGT1A8ENST00000373450.5 linkuse as main transcriptc.855+53872T>C intron_variant 1 NM_019076.5 ENSP00000362549 P1Q9HAW9-1
UGT1A10ENST00000373445.1 linkuse as main transcriptc.855+35057T>C intron_variant 1 ENSP00000362544 Q9HAW8-2

Frequencies

GnomAD3 genomes
AF:
0.00104
AC:
159
AN:
152188
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00308
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000282
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00143
Gnomad OTH
AF:
0.000955
GnomAD3 exomes
AF:
0.000920
AC:
231
AN:
251094
Hom.:
1
AF XY:
0.000980
AC XY:
133
AN XY:
135690
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.000954
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000261
Gnomad FIN exome
AF:
0.000277
Gnomad NFE exome
AF:
0.00142
Gnomad OTH exome
AF:
0.00359
GnomAD4 exome
AF:
0.000917
AC:
1340
AN:
1461670
Hom.:
3
Cov.:
33
AF XY:
0.000895
AC XY:
651
AN XY:
727144
show subpopulations
Gnomad4 AFR exome
AF:
0.000239
Gnomad4 AMR exome
AF:
0.00130
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000255
Gnomad4 FIN exome
AF:
0.000543
Gnomad4 NFE exome
AF:
0.00105
Gnomad4 OTH exome
AF:
0.000878
GnomAD4 genome
AF:
0.00104
AC:
159
AN:
152306
Hom.:
1
Cov.:
32
AF XY:
0.00114
AC XY:
85
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.000241
Gnomad4 AMR
AF:
0.00307
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000282
Gnomad4 NFE
AF:
0.00143
Gnomad4 OTH
AF:
0.000945
Alfa
AF:
0.000340
Hom.:
0
Bravo
AF:
0.00134
TwinsUK
AF:
0.000539
AC:
2
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.00151
AC:
13
ExAC
AF:
0.00105
AC:
128
EpiCase
AF:
0.00175
EpiControl
AF:
0.00154

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

UGT1A9-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesAug 15, 2024This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.22
BayesDel_addAF
Benign
-0.45
T
BayesDel_noAF
Benign
-0.46
CADD
Benign
16
DANN
Benign
0.96
DEOGEN2
Benign
0.23
T
Eigen
Benign
-0.63
Eigen_PC
Benign
-0.70
FATHMM_MKL
Benign
0.077
N
LIST_S2
Benign
0.59
T
M_CAP
Benign
0.0064
T
MetaRNN
Benign
0.017
T
MetaSVM
Benign
-0.92
T
MutationAssessor
Benign
1.3
L
MutationTaster
Benign
1.0
N;N;N;N
PROVEAN
Benign
-1.7
N
REVEL
Benign
0.13
Sift
Uncertain
0.014
D
Sift4G
Benign
0.087
T
Polyphen
0.35
B
Vest4
0.18
MVP
0.20
MPC
0.082
ClinPred
0.016
T
GERP RS
3.4
Varity_R
0.19
gMVP
0.23

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs151238339; hg19: chr2-234581080; API