Genetic Variant ENSG00000299813:n.52-4236G>A (chr4-69051355-C-T) – 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.52-4236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,082 control chromosomes in the GnomAD database, including 17,806 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 ( 17799 hom., cov: 32)

Exomes 𝑓: 0.44 ( 7 hom. )

Consequence

ENSG00000299813
ENST00000766642.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.14

Publications

3 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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new If you want to explore the variant's impact on the transcript ENST00000766642.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766642.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2B7	NM_001349568.2		c.-406C>T		upstream_gene	N/A	NP_001336497.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENSG00000299813	ENST00000766642.1		n.52-4236G>A	intron	N/A
UGT2B7	ENST00000502942.5	TSL:2	c.-406C>T	upstream_gene	N/A	ENSP00000426206.1	D6RH08
UGT2B7	ENST00000509763.1	TSL:5	n.-121C>T	upstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.463

AC:

70337

AN:

151910

Hom.:

17775

Cov.:

show subpopulations

Gnomad AFR

AF:

0.665

Gnomad AMI

AF:

0.327

Gnomad AMR

AF:

0.427

Gnomad ASJ

AF:

0.514

Gnomad EAS

AF:

0.577

Gnomad SAS

AF:

0.428

Gnomad FIN

AF:

0.358

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.357

Gnomad OTH

AF:

0.469

GnomAD4 exome

AF:

0.442

AC:

AN:

Hom.:

Cov.:

AF XY:

0.447

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)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.523

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.463

AC:

70405

AN:

152030

Hom.:

17799

Cov.:

AF XY:

0.463

AC XY:

34389

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.665

AC:

27574

AN:

41456

American (AMR)

AF:

0.426

AC:

6510

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.514

AC:

1780

AN:

3466

East Asian (EAS)

AF:

0.577

AC:

2973

AN:

5156

South Asian (SAS)

AF:

0.429

AC:

2066

AN:

4820

European-Finnish (FIN)

AF:

0.358

AC:

3792

AN:

10578

Middle Eastern (MID)

AF:

0.531

AC:

156

AN:

294

European-Non Finnish (NFE)

AF:

0.357

AC:

24266

AN:

67958

Other (OTH)

AF:

0.468

AC:

990

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1823

3646

5470

7293

9116

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

626

1252

1878

2504

3130

<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:

0.444

Hom.:

2456

Bravo

AF:

0.477

Asia WGS

AF:

0.479

AC:

1664

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

5.4

(source)

DANN

Benign

0.61

PhyloP100

-2.1

PromoterAI

-0.047

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over