Variant chr4-69489575-GA-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_021139.3(UGT2B4):c.871-6del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 1,595,084 control chromosomes in the GnomAD database, including 35 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0015 ( 7 hom., cov: 32)

Exomes 𝑓: 0.0012 ( 28 hom. )

Consequence

UGT2B4
NM_021139.3 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.77

Variant links:

Genes affected

UGT2B4 (HGNC:12553): (UDP glucuronosyltransferase family 2 member B4) Enables glucuronosyltransferase activity. Involved in cellular glucuronidation and estrogen metabolic process. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

UGT2B4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 4-69489575-GA-G is Benign according to our data. Variant chr4-69489575-GA-G is described in ClinVar as [Benign]. Clinvar id is 717904.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00146 (221/151202) while in subpopulation EAS AF= 0.041 (210/5128). AF 95% confidence interval is 0.0364. There are 7 homozygotes in gnomad4. There are 120 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
UGT2B4	NM_021139.3 linkuse as main transcript	c.871-6del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	ENST00000305107.7	NP_066962.2
UGT2B4	NM_001297615.2 linkuse as main transcript	c.871-6del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		NP_001284544.1
UGT2B4	NM_001297616.2 linkuse as main transcript	c.463-6del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		NP_001284545.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGT2B4	ENST00000305107.7 linkuse as main transcript	c.871-6del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_021139.3	ENSP00000305221	P1	P06133-1

Frequencies

GnomAD3 genomes

AF:

0.00147

AC:

222

AN:

151084

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000243

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000660

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0411

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000148

Gnomad OTH

AF:

0.00145

GnomAD3 exomes

AF:

0.00297

AC:

697

AN:

234660

Hom.:

AF XY:

0.00278

AC XY:

354

AN XY:

127550

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000337

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0399

Gnomad SAS exome

AF:

0.000398

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000276

Gnomad OTH exome

AF:

0.00194

GnomAD4 exome

AF:

0.00118

AC:

1702

AN:

1443882

Hom.:

Cov.:

AF XY:

0.00112

AC XY:

806

AN XY:

718510

show subpopulations

Gnomad4 AFR exome

AF:

0.0000314

Gnomad4 AMR exome

AF:

0.0000500

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0386

Gnomad4 SAS exome

AF:

0.000514

Gnomad4 FIN exome

AF:

0.0000378

Gnomad4 NFE exome

AF:

0.0000190

Gnomad4 OTH exome

AF:

0.00187

GnomAD4 genome

AF:

0.00146

AC:

221

AN:

151202

Hom.:

Cov.:

AF XY:

0.00163

AC XY:

120

AN XY:

73796

show subpopulations

Gnomad4 AFR

AF:

0.0000243

Gnomad4 AMR

AF:

0.0000659

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0410

Gnomad4 SAS

AF:

0.00125

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000148

Gnomad4 OTH

AF:

0.000954

Alfa

AF:

0.000218

Hom.:

Bravo

AF:

0.00172

EpiCase

AF:

0.000111

EpiControl

AF:

0.00

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Apr 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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