4-69493127-T-G

Position:

• chr4-69493127-T-G

Variant summary

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

The NM_021139.3(UGT2B4):​c.870+566A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,926 control chromosomes in the GnomAD database, including 3,874 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 0.21 (3874 hom., cov: 31)
• Consequence: UGT2B4 NM_021139.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UGT2B4	NM_021139.3	c.870+566A>C		intron_variant		ENST00000305107.7	NP_066962.2
UGT2B4	NM_001297616.2	c.462+566A>C		intron_variant			NP_001284545.1
UGT2B4	NM_001297615.2	c.870+566A>C		intron_variant			NP_001284544.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGT2B4	ENST00000305107.7	c.870+566A>C		intron_variant		1	NM_021139.3	ENSP00000305221.6

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31589 AN: 151810 Hom.: 3881 Cov.: 31

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.208 AC: 31591 AN: 151926 Hom.: 3874 Cov.: 31 AF XY: 0.215 AC XY: 15959 AN XY: 74204

Gnomad4 AFR AF: 0.0999

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.0187

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.208

Alfa AF: 0.205 Hom.: 1163

Bravo AF: 0.193

Asia WGS AF: 0.159 AC: 553 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.48

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: rs17671289; hg19: chr4-70358845;