NM_001077.4:c.826G>C

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4

The NM_001077.4(UGT2B17):ā€‹c.826G>Cā€‹(p.Asp276His) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/21 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: not found (cov: 20)
Exomes š‘“: 0.0000016 ( 1 hom. )
Failed GnomAD Quality Control

Consequence

UGT2B17
NM_001077.4 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.48
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.27285895).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
UGT2B17NM_001077.4 linkc.826G>C p.Asp276His missense_variant Exon 3 of 7 ENST00000317746.3 NP_001068.1 O75795

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
UGT2B17ENST00000317746.3 linkc.826G>C p.Asp276His missense_variant Exon 3 of 7 1 NM_001077.4 ENSP00000320401.2 O75795
UGT2B17ENST00000684088.1 linkc.76G>C p.Asp26His missense_variant Exon 2 of 5 ENSP00000507374.1 A0A804HJ67

Frequencies

GnomAD3 genomes
Cov.:
20
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000160
AC:
2
AN:
1246262
Hom.:
1
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
615786
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000537
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.32
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.44
CADD
Benign
15
DANN
Benign
0.70
DEOGEN2
Benign
0.18
T
Eigen
Benign
-0.36
Eigen_PC
Benign
-0.42
FATHMM_MKL
Benign
0.66
D
LIST_S2
Benign
0.78
T
M_CAP
Benign
0.0034
T
MetaRNN
Benign
0.27
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.9
L
PrimateAI
Benign
0.39
T
PROVEAN
Uncertain
-2.4
N
REVEL
Benign
0.11
Sift
Benign
0.084
T
Sift4G
Benign
0.56
T
Vest4
0.29
MutPred
0.62
Loss of stability (P = 0.0711);
MVP
0.28
MPC
1.2
ClinPred
0.52
D
GERP RS
1.8
Varity_R
0.10
gMVP
0.36

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs769625320; hg19: chr4-69431337; API