NM_001077.4:c.541G>T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_001077.4(UGT2B17):​c.541G>T​(p.Val181Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000152 in 1,380,616 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000016 ( 0 hom., cov: 20)
Exomes 𝑓: 0.000015 ( 4 hom. )

Consequence

UGT2B17
NM_001077.4 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.91
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.057076752).
BS2
High Homozygotes in GnomAdExome4 at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
UGT2B17NM_001077.4 linkc.541G>T p.Val181Phe missense_variant Exon 2 of 7 ENST00000317746.3 NP_001068.1 O75795

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
UGT2B17ENST00000317746.3 linkc.541G>T p.Val181Phe missense_variant Exon 2 of 7 1 NM_001077.4 ENSP00000320401.2 O75795
UGT2B17ENST00000684088.1 linkc.-26-2224G>T intron_variant Intron 1 of 4 ENSP00000507374.1 A0A804HJ67

Frequencies

GnomAD3 genomes
AF:
0.0000158
AC:
2
AN:
126652
Hom.:
0
Cov.:
20
show subpopulations
Gnomad AFR
AF:
0.0000270
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000168
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000199
AC:
4
AN:
201108
Hom.:
2
AF XY:
0.0000185
AC XY:
2
AN XY:
108290
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000396
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000152
AC:
19
AN:
1253964
Hom.:
4
Cov.:
29
AF XY:
0.00000967
AC XY:
6
AN XY:
620410
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000186
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000171
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000158
AC:
2
AN:
126652
Hom.:
0
Cov.:
20
AF XY:
0.0000165
AC XY:
1
AN XY:
60436
show subpopulations
Gnomad4 AFR
AF:
0.0000270
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000168
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.0000669
AC:
7

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.17
BayesDel_addAF
Benign
-0.35
T
BayesDel_noAF
Benign
-0.62
CADD
Benign
0.0020
DANN
Benign
0.22
DEOGEN2
Benign
0.039
T
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.8
FATHMM_MKL
Benign
0.0042
N
LIST_S2
Benign
0.015
T
M_CAP
Benign
0.00095
T
MetaRNN
Benign
0.057
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.035
N
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-0.040
N
REVEL
Benign
0.045
Sift
Benign
0.55
T
Sift4G
Benign
0.34
T
Vest4
0.12
MutPred
0.52
Gain of glycosylation at T180 (P = 0.0306);
MVP
0.29
MPC
0.12
ClinPred
0.040
T
GERP RS
-5.3
Varity_R
0.030
gMVP
0.33

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: rs72551386; hg19: chr4-69433662; API