4-68550840-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PP3_Strong
The NM_001077.4(UGT2B17):c.1150G>A(p.Ala384Thr) variant causes a missense change. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A384A) has been classified as Benign.
Frequency
Genomes: not found (cov: 20)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
UGT2B17
NM_001077.4 missense
NM_001077.4 missense
Scores
5
10
3
Clinical Significance
Conservation
PhyloP100: 7.00
Publications
0 publications found
Genes affected
UGT2B17 (HGNC:12547): (UDP glucuronosyltransferase family 2 member B17) This gene encodes a member of the uridine diphosphoglucuronosyltransferase protein family. The encoded enzyme catalyzes the transfer of glucuronic acid from uridine diphosphoglucuronic acid to a diverse array of substrates including steroid hormones and lipid-soluble drugs. This process, known as glucuronidation, is an intermediate step in the metabolism of steroids. Copy number variation in this gene is associated with susceptibility to osteoporosis.[provided by RefSeq, Apr 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.947
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001077.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| UGT2B17 | TSL:1 MANE Select | c.1150G>A | p.Ala384Thr | missense | Exon 6 of 7 | ENSP00000320401.2 | O75795 | ||
| UGT2B17 | c.1150G>A | p.Ala384Thr | missense | Exon 5 of 6 | ENSP00000563293.1 | ||||
| UGT2B17 | c.1018G>A | p.Ala340Thr | missense | Exon 4 of 5 | ENSP00000620938.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
20
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1252124Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 618410
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1252124
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
618410
African (AFR)
AF:
AC:
0
AN:
30838
American (AMR)
AF:
AC:
0
AN:
36576
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22330
East Asian (EAS)
AF:
AC:
0
AN:
10790
South Asian (SAS)
AF:
AC:
0
AN:
56290
European-Finnish (FIN)
AF:
AC:
0
AN:
41832
Middle Eastern (MID)
AF:
AC:
0
AN:
4866
European-Non Finnish (NFE)
AF:
AC:
0
AN:
997604
Other (OTH)
AF:
AC:
0
AN:
50998
GnomAD4 genome
GnomAD4 genome
Cov.:
20
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Vest4
MutPred
Gain of catalytic residue at A384 (P = 0.0654)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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