Genetic Variant ENSG00000299813:n.52-4203C>T (chr4-69051322-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000766642.1(ENSG00000299813):n.52-4203C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,102 control chromosomes in the GnomAD database, including 17,533 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 0.46 ( 17527 hom., cov: 32)

Exomes 𝑓: 0.30 ( 6 hom. )

Consequence

ENSG00000299813
ENST00000766642.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0640

Publications

2 publications found

Variant links:

Genes affected

ENSG00000299813 (HGNC:58801):

ENSG00000299813 links:

LOC105377265 (HGNC:):

LOC105377265 links:

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 was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105377265	XR_001741714.2 link	n.3048-1186C>T	intron_variant	Intron 2 of 4
LOC105377265	XR_938851.2 link	n.316-1186C>T	intron_variant	Intron 1 of 3
LOC105377265	XR_938852.2 link	n.316-1294C>T	intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
ENSG00000299813	ENST00000766642.1 link	n.52-4203C>T	intron_variant	Intron 1 of 1
UGT2B7	ENST00000502942.5 link	c.-439G>A	upstream_gene_variant		2	ENSP00000426206.1
UGT2B7	ENST00000509763.1 link	n.-154G>A	upstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.460

AC:

69909

AN:

151904

Hom.:

17505

Cov.:

show subpopulations

Gnomad AFR

AF:

0.654

Gnomad AMI

AF:

0.327

Gnomad AMR

AF:

0.426

Gnomad ASJ

AF:

0.513

Gnomad EAS

AF:

0.578

Gnomad SAS

AF:

0.429

Gnomad FIN

AF:

0.359

Gnomad MID

AF:

0.528

Gnomad NFE

AF:

0.357

Gnomad OTH

AF:

0.467

GnomAD4 exome

AF:

0.300

AC:

AN:

Hom.:

Cov.:

AF XY:

0.354

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.167

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.354

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.460

AC:

69975

AN:

152022

Hom.:

17527

Cov.:

AF XY:

0.460

AC XY:

34207

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.655

AC:

27152

AN:

41474

American (AMR)

AF:

0.425

AC:

6499

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.513

AC:

1780

AN:

3468

East Asian (EAS)

AF:

0.577

AC:

2976

AN:

5158

South Asian (SAS)

AF:

0.430

AC:

2066

AN:

4810

European-Finnish (FIN)

AF:

0.359

AC:

3785

AN:

10548

Middle Eastern (MID)

AF:

0.534

AC:

157

AN:

294

European-Non Finnish (NFE)

AF:

0.357

AC:

24279

AN:

67962

Other (OTH)

AF:

0.465

AC:

983

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1847

3693

5540

7386

9233

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<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:

0.399

Hom.:

1675

Bravo

AF:

0.474

Asia WGS

AF:

0.478

AC:

1662

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.5

(source)

DANN

Benign

0.64

PhyloP100

0.064

PromoterAI

-0.0070

Neutral

(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