Genetic Variant UGT2B17:p.Tyr355Tyr (chr4-68551852-A-G) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001077.4(UGT2B17):c.1065T>C(p.Tyr355Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 1,360,418 control chromosomes in the GnomAD database, including 347,751 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.56 ( 26770 hom., cov: 20)

Exomes 𝑓: 0.63 ( 320981 hom. )

Consequence

UGT2B17
NM_001077.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.910

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 -14 ACMG points.

BP4

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

BP6

Variant 4-68551852-A-G is Benign according to our data. Variant chr4-68551852-A-G is described in ClinVar as [Benign]. Clinvar id is 3059019.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.91 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT2B17	NM_001077.4 link	c.1065T>C	p.Tyr355Tyr	synonymous_variant	Exon 5 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.1065T>C	p.Tyr355Tyr	synonymous_variant	Exon 5 of 7	1	NM_001077.4	ENSP00000320401.2		O75795
UGT2B17	ENST00000684088.1 link	c.315T>C	p.Tyr105Tyr	synonymous_variant	Exon 4 of 5			ENSP00000507374.1		A0A804HJ67

Frequencies

GnomAD3 genomes

AF:

0.557

AC:

68751

AN:

123516

Hom.:

26764

Cov.:

show subpopulations

Gnomad AFR

AF:

0.387

Gnomad AMI

AF:

0.587

Gnomad AMR

AF:

0.520

Gnomad ASJ

AF:

0.703

Gnomad EAS

AF:

0.654

Gnomad SAS

AF:

0.536

Gnomad FIN

AF:

0.559

Gnomad MID

AF:

0.831

Gnomad NFE

AF:

0.657

Gnomad OTH

AF:

0.615

GnomAD3 exomes

AF:

0.593

AC:

118401

AN:

199732

Hom.:

48827

AF XY:

0.605

AC XY:

64898

AN XY:

107318

show subpopulations

Gnomad AFR exome

AF:

0.379

Gnomad AMR exome

AF:

0.417

Gnomad ASJ exome

AF:

0.698

Gnomad EAS exome

AF:

0.698

Gnomad SAS exome

AF:

0.549

Gnomad FIN exome

AF:

0.582

Gnomad NFE exome

AF:

0.668

Gnomad OTH exome

AF:

0.648

GnomAD4 exome

AF:

0.631

AC:

780508

AN:

1236842

Hom.:

320981

Cov.:

AF XY:

0.632

AC XY:

386009

AN XY:

611244

show subpopulations

Gnomad4 AFR exome

AF:

0.382

Gnomad4 AMR exome

AF:

0.429

Gnomad4 ASJ exome

AF:

0.686

Gnomad4 EAS exome

AF:

0.699

Gnomad4 SAS exome

AF:

0.540

Gnomad4 FIN exome

AF:

0.573

Gnomad4 NFE exome

AF:

0.651

Gnomad4 OTH exome

AF:

0.638

GnomAD4 genome

AF:

0.557

AC:

68775

AN:

123576

Hom.:

26770

Cov.:

AF XY:

0.552

AC XY:

32506

AN XY:

58862

show subpopulations

Gnomad4 AFR

AF:

0.387

Gnomad4 AMR

AF:

0.519

Gnomad4 ASJ

AF:

0.703

Gnomad4 EAS

AF:

0.655

Gnomad4 SAS

AF:

0.538

Gnomad4 FIN

AF:

0.559

Gnomad4 NFE

AF:

0.657

Gnomad4 OTH

AF:

0.619

Alfa

AF:

0.747

Hom.:

6361

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

UGT2B17-related disorder

Benign:1

Oct 21, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.87

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

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