Variant chr4-68550838-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001077.4(UGT2B17):c.1152A>G(p.Ala384=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 1,303,652 control chromosomes in the GnomAD database, including 140,188 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.27 ( 10648 hom., cov: 20)

Exomes 𝑓: 0.31 ( 129540 hom. )

Consequence

UGT2B17
NM_001077.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.93

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 4-68550838-T-C is Benign according to our data. Variant chr4-68550838-T-C is described in ClinVar as [Benign]. Clinvar id is 3059332.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.93 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGT2B17	NM_001077.4 linkuse as main transcript	c.1152A>G	p.Ala384=	synonymous_variant	6/7	ENST00000317746.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGT2B17	ENST00000317746.3 linkuse as main transcript	c.1152A>G	p.Ala384=	synonymous_variant	6/7	1	NM_001077.4	P1
UGT2B17	ENST00000684088.1 linkuse as main transcript	c.402A>G	p.Ala134=	synonymous_variant	5/5

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

32978

AN:

124396

Hom.:

10644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0971

Gnomad AMI

AF:

0.589

Gnomad AMR

AF:

0.403

Gnomad ASJ

AF:

0.237

Gnomad EAS

AF:

0.0113

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.400

Gnomad MID

AF:

0.131

Gnomad NFE

AF:

0.329

Gnomad OTH

AF:

0.238

GnomAD3 exomes

AF:

0.295

AC:

55653

AN:

188972

Hom.:

20352

AF XY:

0.291

AC XY:

29476

AN XY:

101340

show subpopulations

Gnomad AFR exome

AF:

0.0844

Gnomad AMR exome

AF:

0.517

Gnomad ASJ exome

AF:

0.190

Gnomad EAS exome

AF:

0.00591

Gnomad SAS exome

AF:

0.276

Gnomad FIN exome

AF:

0.370

Gnomad NFE exome

AF:

0.281

Gnomad OTH exome

AF:

0.275

GnomAD4 exome

AF:

0.307

AC:

362273

AN:

1179192

Hom.:

129540

Cov.:

AF XY:

0.306

AC XY:

178413

AN XY:

582660

show subpopulations

Gnomad4 AFR exome

AF:

0.0765

Gnomad4 AMR exome

AF:

0.504

Gnomad4 ASJ exome

AF:

0.231

Gnomad4 EAS exome

AF:

0.00464

Gnomad4 SAS exome

AF:

0.313

Gnomad4 FIN exome

AF:

0.396

Gnomad4 NFE exome

AF:

0.311

Gnomad4 OTH exome

AF:

0.278

GnomAD4 genome

AF:

0.265

AC:

32991

AN:

124460

Hom.:

10648

Cov.:

AF XY:

0.269

AC XY:

16004

AN XY:

59400

show subpopulations

Gnomad4 AFR

AF:

0.0972

Gnomad4 AMR

AF:

0.404

Gnomad4 ASJ

AF:

0.237

Gnomad4 EAS

AF:

0.0113

Gnomad4 SAS

AF:

0.278

Gnomad4 FIN

AF:

0.400

Gnomad4 NFE

AF:

0.329

Gnomad4 OTH

AF:

0.234

Alfa

AF:

0.0314

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

UGT2B17-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

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

-0.82

CADD

Benign

0.14

DANN

Benign

0.30

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