rs7435827

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001077.4(UGT2B17):​c.1313+1451T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.48 ( 22680 hom., cov: 19)

Consequence

UGT2B17
NM_001077.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.87
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
UGT2B17NM_001077.4 linkuse as main transcriptc.1313+1451T>C intron_variant ENST00000317746.3 NP_001068.1 O75795

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UGT2B17ENST00000317746.3 linkuse as main transcriptc.1313+1451T>C intron_variant 1 NM_001077.4 ENSP00000320401.2 O75795

Frequencies

GnomAD3 genomes
AF:
0.483
AC:
58545
AN:
121320
Hom.:
22688
Cov.:
19
show subpopulations
Gnomad AFR
AF:
0.170
Gnomad AMI
AF:
0.593
Gnomad AMR
AF:
0.491
Gnomad ASJ
AF:
0.636
Gnomad EAS
AF:
0.585
Gnomad SAS
AF:
0.515
Gnomad FIN
AF:
0.561
Gnomad MID
AF:
0.758
Gnomad NFE
AF:
0.650
Gnomad OTH
AF:
0.539
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.482
AC:
58525
AN:
121382
Hom.:
22680
Cov.:
19
AF XY:
0.477
AC XY:
27475
AN XY:
57578
show subpopulations
Gnomad4 AFR
AF:
0.170
Gnomad4 AMR
AF:
0.490
Gnomad4 ASJ
AF:
0.636
Gnomad4 EAS
AF:
0.584
Gnomad4 SAS
AF:
0.517
Gnomad4 FIN
AF:
0.561
Gnomad4 NFE
AF:
0.650
Gnomad4 OTH
AF:
0.544
Alfa
AF:
0.509
Hom.:
2273
Asia WGS
AF:
0.592
AC:
1101
AN:
1862

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
5.3
DANN
Benign
0.55

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: rs7435827; hg19: chr4-69414944; API