Genetic Variant UGT2B17:p.Leu289Leu (chr4-68565580-A-G) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001077.4(UGT2B17):c.865T>C(p.Leu289Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00066 in 1,369,026 control chromosomes in the GnomAD database, including 220 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0010 ( 29 hom., cov: 20)

Exomes 𝑓: 0.00062 ( 191 hom. )

Consequence

UGT2B17
NM_001077.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:2

Conservation

PhyloP100: 1.35

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]

UGT2B17 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 4-68565580-A-G is Benign according to our data. Variant chr4-68565580-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 709197.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.35 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 29 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT2B17	NM_001077.4 link	c.865T>C	p.Leu289Leu	synonymous_variant	Exon 3 of 7	ENST00000317746.3	NP_001068.1	O75795

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B17	ENST00000317746.3 link	c.865T>C	p.Leu289Leu	synonymous_variant	Exon 3 of 7	1	NM_001077.4	ENSP00000320401.2		O75795
UGT2B17	ENST00000684088.1 link	c.115T>C	p.Leu39Leu	synonymous_variant	Exon 2 of 5			ENSP00000507374.1		A0A804HJ67

Frequencies

GnomAD3 genomes

AF:

0.00102

AC:

128

AN:

125488

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00152

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000986

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00150

Gnomad SAS

AF:

0.000737

Gnomad FIN

AF:

0.000273

Gnomad MID

AF:

0.00362

Gnomad NFE

AF:

0.000823

Gnomad OTH

AF:

0.00237

GnomAD3 exomes

AF:

0.000763

AC:

149

AN:

195272

Hom.:

AF XY:

0.000638

AC XY:

AN XY:

105026

show subpopulations

Gnomad AFR exome

AF:

0.00122

Gnomad AMR exome

AF:

0.00138

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000321

Gnomad FIN exome

AF:

0.000415

Gnomad NFE exome

AF:

0.000789

Gnomad OTH exome

AF:

0.000400

GnomAD4 exome

AF:

0.000625

AC:

777

AN:

1243470

Hom.:

191

Cov.:

AF XY:

0.000610

AC XY:

375

AN XY:

614356

show subpopulations

Gnomad4 AFR exome

AF:

0.00105

Gnomad4 AMR exome

AF:

0.00122

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000194

Gnomad4 SAS exome

AF:

0.000144

Gnomad4 FIN exome

AF:

0.000336

Gnomad4 NFE exome

AF:

0.000646

Gnomad4 OTH exome

AF:

0.000592

GnomAD4 genome

AF:

0.00100

AC:

126

AN:

125556

Hom.:

Cov.:

AF XY:

0.000984

AC XY:

AN XY:

59930

show subpopulations

Gnomad4 AFR

AF:

0.00149

Gnomad4 AMR

AF:

0.000985

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00151

Gnomad4 SAS

AF:

0.000741

Gnomad4 FIN

AF:

0.000273

Gnomad4 NFE

AF:

0.000823

Gnomad4 OTH

AF:

0.00235

Alfa

AF:

0.000818

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

UGT2B17-related disorder

Benign:1

Oct 31, 2019

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This 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). -

not provided

Benign:1

Jun 29, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.9

DANN

Benign

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over