rs17147016

chr4-68929508-T-Achr4-68929508-T-C

Variant summary

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

The NM_024743.4(UGT2A3):c.*305A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 214,190 control chromosomes in the GnomAD database, including 4,705 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 (3497 hom., cov: 32)
  • Exomes 𝑓: 0.18 (1208 hom.)
• Consequence: UGT2A3 NM_024743.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

UGT2A3 (HGNC:28528): (UDP glucuronosyltransferase family 2 member A3) Enables glucuronosyltransferase activity. Involved in cellular glucuronidation. 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGT2A3	NM_024743.4	c.*305A>T		3_prime_UTR_variant	6/6	ENST00000251566.9
UGT2A3	XM_011532247.3	c.*305A>T		3_prime_UTR_variant	6/6
UGT2A3	XM_047416177.1	c.*305A>T		3_prime_UTR_variant	6/6
UGT2A3	NR_024010.2	n.2030A>T		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGT2A3	ENST00000251566.9	c.*305A>T		3_prime_UTR_variant	6/6	1	NM_024743.4	P1
UGT2A3	ENST00000503012.1	c.*1065A>T		3_prime_UTR_variant, NMD_transcript_variant	7/7	2

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31935 AN: 151898 Hom.: 3497 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.228

GnomAD4 exome AF: 0.184 AC: 11433 AN: 62174 Hom.: 1208 Cov.: 0 AF XY: 0.181 AC XY: 5712 AN XY: 31516

Gnomad4 AFR exome AF: 0.205

Gnomad4 AMR exome AF: 0.170

Gnomad4 ASJ exome AF: 0.263

Gnomad4 EAS exome AF: 0.307

Gnomad4 SAS exome AF: 0.124

Gnomad4 FIN exome AF: 0.133

Gnomad4 NFE exome AF: 0.170

Gnomad4 OTH exome AF: 0.193

GnomAD4 genome AF: 0.210 AC: 31944 AN: 152016 Hom.: 3497 Cov.: 32 AF XY: 0.211 AC XY: 15687 AN XY: 74306

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.225

Alfa AF: 0.192 Hom.: 366

Bravo AF: 0.221

Asia WGS AF: 0.235 AC: 815 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.0
Dann	Benign	0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs17147016; hg19: chr4-69795226;