dbSNP rs7668282: UGT2B7:c.-26-2144T>C (chr4-69096396-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001349568.2(UGT2B7):c.-26-2144T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0171 in 1,439,516 control chromosomes in the GnomAD database, including 922 homozygotes. 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 0.025 ( 114 hom., cov: 32)

Exomes 𝑓: 0.016 ( 808 hom. )

Consequence

UGT2B7
NM_001349568.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.124

Publications

21 publications found

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:

ENSG00000299782 (HGNC:):

ENSG00000299782 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
UGT2B7	NM_001349568.2 link	c.-26-2144T>C	intron_variant	Intron 2 of 6		NP_001336497.1
UGT2B7	NM_001074.4 link	c.-125T>C	upstream_gene_variant		ENST00000305231.12	NP_001065.2	P16662
UGT2B7	NM_001330719.2 link	c.-125T>C	upstream_gene_variant			NP_001317648.1	P16662E9PBP8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B7	ENST00000305231.12 link	c.-125T>C		upstream_gene_variant		1	NM_001074.4	ENSP00000304811.7		P16662

Frequencies

GnomAD3 genomes

AF:

0.0245

AC:

3736

AN:

152180

Hom.:

113

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0431

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0253

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.0816

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.00358

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00692

Gnomad OTH

AF:

0.0201

GnomAD4 exome

AF:

0.0162

AC:

20867

AN:

1287218

Hom.:

808

AF XY:

0.0187

AC XY:

11945

AN XY:

640448

show subpopulations

African (AFR)

AF:

0.0436

AC:

1240

AN:

28444

American (AMR)

AF:

0.0254

AC:

728

AN:

28668

Ashkenazi Jewish (ASJ)

AF:

0.00386

AC:

AN:

20978

East Asian (EAS)

AF:

0.0830

AC:

3177

AN:

38256

South Asian (SAS)

AF:

0.115

AC:

8121

AN:

70846

European-Finnish (FIN)

AF:

0.00386

AC:

188

AN:

48656

Middle Eastern (MID)

AF:

0.0205

AC:

108

AN:

5266

European-Non Finnish (NFE)

AF:

0.00620

AC:

6146

AN:

992052

Other (OTH)

AF:

0.0199

AC:

1078

AN:

54052

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

970

1939

2909

3878

4848

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

378

756

1134

1512

1890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0246

AC:

3741

AN:

152298

Hom.:

114

Cov.:

AF XY:

0.0274

AC XY:

2037

AN XY:

74468

show subpopulations

African (AFR)

AF:

0.0430

AC:

1789

AN:

41574

American (AMR)

AF:

0.0254

AC:

389

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.00259

AC:

AN:

3472

East Asian (EAS)

AF:

0.0816

AC:

423

AN:

5182

South Asian (SAS)

AF:

0.119

AC:

575

AN:

4814

European-Finnish (FIN)

AF:

0.00358

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00692

AC:

471

AN:

68020

Other (OTH)

AF:

0.0199

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

179

359

538

718

897

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0144

Hom.:

103

Bravo

AF:

0.0250

Asia WGS

AF:

0.102

AC:

353

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.7

(source)

DANN

Benign

0.68

PhyloP100

0.12

PromoterAI

0.042

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over