Genetic Variant UGT2B4:c.44-613T>A (chr4-69496023-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001297616.2(UGT2B4):c.44-613T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000276 in 1,088,326 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.0000028 ( 0 hom. )

Consequence

UGT2B4
NM_001297616.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.414

Publications

0 publications found

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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
UGT2B4	NM_001297616.2 link	c.44-613T>A	intron_variant	Intron 1 of 6		NP_001284545.1	P06133-2
UGT2B4	NM_021139.3 link	c.-162T>A	upstream_gene_variant		ENST00000305107.7	NP_066962.2	P06133-1
UGT2B4	NM_001297615.2 link	c.-162T>A	upstream_gene_variant			NP_001284544.1	P06133-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B4	ENST00000305107.7 link	c.-162T>A		upstream_gene_variant		1	NM_021139.3	ENSP00000305221.6		P06133-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000276

AC:

AN:

1088326

Hom.:

AF XY:

0.00000561

AC XY:

AN XY:

534968

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

23848

American (AMR)

AF:

0.00

AC:

AN:

19982

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17066

East Asian (EAS)

AF:

0.00

AC:

AN:

33846

South Asian (SAS)

AF:

0.0000210

AC:

AN:

47668

European-Finnish (FIN)

AF:

0.00

AC:

AN:

33044

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4694

European-Non Finnish (NFE)

AF:

0.00000232

AC:

AN:

861794

Other (OTH)

AF:

0.00

AC:

AN:

46384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.608

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.23

(source)

DANN

Benign

0.37

PhyloP100

-0.41

PromoterAI

-0.030

Neutral

(source)

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over