rs2047176

chr5-36056698-C-T

Variant summary

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

The NM_174914.4(UGT3A2):c.197-4714G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,196 control chromosomes in the GnomAD database, including 29,686 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 0.57 (29686 hom., cov: 33)
• Consequence: UGT3A2 NM_174914.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

Genes affected

UGT3A2 (HGNC:27266): (UDP glycosyltransferase family 3 member A2) Enables UDP-glycosyltransferase activity. Acts upstream of or within cellular response to genistein. 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGT3A2	NM_174914.4	c.197-4714G>A		intron_variant		ENST00000282507.8
UGT3A2	NM_001168316.2	c.95-4714G>A		intron_variant
UGT3A2	XM_011513988.2	c.197-1637G>A		intron_variant
UGT3A2	NR_031764.2	n.290-4714G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGT3A2	ENST00000282507.8	c.197-4714G>A		intron_variant		1	NM_174914.4	P1

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87466 AN: 152078 Hom.: 29701 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.575 AC: 87451 AN: 152196 Hom.: 29686 Cov.: 33 AF XY: 0.579 AC XY: 43092 AN XY: 74400

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.598

Alfa AF: 0.708 Hom.: 55771

Bravo AF: 0.537

Asia WGS AF: 0.476 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	6.7
Dann	Benign	0.46

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: rs2047176; hg19: chr5-36056800;