rs2013562

Positions:

• chr4-69488857-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021139.3(UGT2B4):​c.1002+582G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,644 control chromosomes in the GnomAD database, including 13,288 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 0.41 (13288 hom., cov: 30)
• Consequence: UGT2B4 NM_021139.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGT2B4	NM_021139.3	c.1002+582G>A		intron_variant		ENST00000305107.7
UGT2B4	NM_001297615.2	c.1002+582G>A		intron_variant
UGT2B4	NM_001297616.2	c.594+582G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGT2B4	ENST00000305107.7	c.1002+582G>A		intron_variant		1	NM_021139.3	P1
UGT2B4	ENST00000512583.5	c.1002+582G>A		intron_variant		1
UGT2B4	ENST00000502655.5	n.879+582G>A		intron_variant, non_coding_transcript_variant		5
UGT2B4	ENST00000506580.5	n.784+582G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61640 AN: 151526 Hom.: 13283 Cov.: 30

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.421

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.407 AC: 61673 AN: 151644 Hom.: 13288 Cov.: 30 AF XY: 0.415 AC XY: 30753 AN XY: 74066

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.421

Alfa AF: 0.440 Hom.: 19976

Bravo AF: 0.396

Asia WGS AF: 0.498 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.21

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

Other links and lift over

dbSNP: rs2013562; hg19: chr4-70354575;