NM_024743.4:c.*305A>T

Variant names:

• chr4-68929508-T-A
• rs17147016
• NM_024743.4:c.*305A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024743.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2A3	NM_024743.4	MANE Select	c.*305A>T		3_prime_UTR	Exon 6 of 6	NP_079019.3
	UGT2A3	NR_024010.2		n.2030A>T		non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2A3	ENST00000251566.9	TSL:1 MANE Select	c.*305A>T		3_prime_UTR	Exon 6 of 6	ENSP00000251566.4
	UGT2A3	ENST00000503012.1	TSL:2	n.*1065A>T		non_coding_transcript_exon	Exon 7 of 7	ENSP00000424092.1
	UGT2A3	ENST00000503012.1	TSL:2	n.*1065A>T		3_prime_UTR	Exon 7 of 7	ENSP00000424092.1

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

African (AFR) AF: 0.205 AC: 511 AN: 2496

American (AMR) AF: 0.170 AC: 634 AN: 3730

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 576 AN: 2192

East Asian (EAS) AF: 0.307 AC: 1493 AN: 4868

South Asian (SAS) AF: 0.124 AC: 282 AN: 2282

European-Finnish (FIN) AF: 0.133 AC: 328 AN: 2470

Middle Eastern (MID) AF: 0.234 AC: 73 AN: 312

European-Non Finnish (NFE) AF: 0.170 AC: 6739 AN: 39684

Other (OTH) AF: 0.193 AC: 797 AN: 4140

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

African (AFR) AF: 0.243 AC: 10069 AN: 41452

American (AMR) AF: 0.218 AC: 3321 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3468

East Asian (EAS) AF: 0.340 AC: 1748 AN: 5136

South Asian (SAS) AF: 0.177 AC: 855 AN: 4820

European-Finnish (FIN) AF: 0.154 AC: 1630 AN: 10600

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.185 AC: 12604 AN: 67966

Other (OTH) AF: 0.225 AC: 476 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.51
PhyloP100		-1.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=96/4	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17147016; hg19: chr4-69795226;