Genetic Variant UGT2B7:p.Thr245Thr (chr4-69098553-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001074.4(UGT2B7):c.735A>G(p.Thr245Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,604,518 control chromosomes in the GnomAD database, including 18,331 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (no stars).

Frequency

Genomes: 𝑓 0.16 ( 2152 hom., cov: 30)

Exomes 𝑓: 0.14 ( 16179 hom. )

Consequence

UGT2B7
NM_001074.4 synonymous

Scores

Clinical Significance

drug response no assertion criteria provided O:1

Conservation

PhyloP100: 0.276

Variant links:

Genes affected

UGT2B7 (HGNC:12554): (UDP glucuronosyltransferase family 2 member B7) The protein encoded by this gene belongs to the UDP-glycosyltransferase (UGT) family. UGTs serve a major role in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This protein is localized in the microsome membrane, and has unique specificity for 3,4-catechol estrogens and estriol, suggesting that it may play an important role in regulating the level and activity of these potent estrogen metabolites. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2017]

UGT2B7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP7

Synonymous conserved (PhyloP=0.276 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT2B7	NM_001074.4 link	c.735A>G	p.Thr245Thr	synonymous_variant	Exon 2 of 6	ENST00000305231.12	NP_001065.2	P16662
UGT2B7	NM_001330719.2 link	c.735A>G	p.Thr245Thr	synonymous_variant	Exon 2 of 5		NP_001317648.1	P16662E9PBP8
UGT2B7	NM_001349568.2 link	c.-13A>G		5_prime_UTR_variant	Exon 3 of 7		NP_001336497.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B7	ENST00000305231.12 link	c.735A>G	p.Thr245Thr	synonymous_variant	Exon 2 of 6	1	NM_001074.4	ENSP00000304811.7		P16662

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

23917

AN:

150748

Hom.:

2149

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.161

Gnomad AMR

AF:

0.275

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.0477

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.244

Gnomad MID

AF:

0.175

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.177

GnomAD3 exomes

AF:

0.172

AC:

42073

AN:

244836

Hom.:

4901

AF XY:

0.162

AC XY:

21491

AN XY:

132718

show subpopulations

Gnomad AFR exome

AF:

0.148

Gnomad AMR exome

AF:

0.383

Gnomad ASJ exome

AF:

0.146

Gnomad EAS exome

AF:

0.0437

Gnomad SAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.248

Gnomad NFE exome

AF:

0.137

Gnomad OTH exome

AF:

0.167

GnomAD4 exome

AF:

0.138

AC:

200354

AN:

1453658

Hom.:

16179

Cov.:

AF XY:

0.136

AC XY:

98393

AN XY:

723090

show subpopulations

Gnomad4 AFR exome

AF:

0.146

Gnomad4 AMR exome

AF:

0.371

Gnomad4 ASJ exome

AF:

0.145

Gnomad4 EAS exome

AF:

0.0609

Gnomad4 SAS exome

AF:

0.122

Gnomad4 FIN exome

AF:

0.245

Gnomad4 NFE exome

AF:

0.127

Gnomad4 OTH exome

AF:

0.137

GnomAD4 genome

AF:

0.159

AC:

23936

AN:

150860

Hom.:

2152

Cov.:

AF XY:

0.165

AC XY:

12137

AN XY:

73594

show subpopulations

Gnomad4 AFR

AF:

0.151

Gnomad4 AMR

AF:

0.275

Gnomad4 ASJ

AF:

0.142

Gnomad4 EAS

AF:

0.0476

Gnomad4 SAS

AF:

0.123

Gnomad4 FIN

AF:

0.244

Gnomad4 NFE

AF:

0.135

Gnomad4 OTH

AF:

0.178

Alfa

AF:

0.117

Hom.:

522

Bravo

AF:

0.164

Asia WGS

AF:

0.115

AC:

399

AN:

3478

ClinVar

Significance: drug response

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Tramadol response

Other:1

Apr 28, 2018

Bruce Budowle Laboratory, University of North Texas Health Science Center

Significance: drug response

Review Status: no assertion criteria provided

Collection Method: research

- T:M1 = postmortem ratio or tramadol to O-desmethyltramadol; t-MP = model-based clustered metabolizer phenotype inferred from T:M1

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.1

DANN

Benign

0.35

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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